diff --git a/benchmarks/BUILD b/benchmarks/BUILD
index 59d3fbf435..766f36644d 100644
--- a/benchmarks/BUILD
+++ b/benchmarks/BUILD
@@ -74,7 +74,6 @@ cc_test(
         "//:protobuf",
         "//src/google/protobuf/json",
         "//upb:base",
-        "//upb:descriptor_upb_proto",
         "//upb:json",
         "//upb:mem",
         "//upb:reflection",
diff --git a/python/BUILD.bazel b/python/BUILD.bazel
index 3e34bbdbc4..e8a7625018 100644
--- a/python/BUILD.bazel
+++ b/python/BUILD.bazel
@@ -191,9 +191,9 @@ py_extension(
     ],
     target_compatible_with = select(_message_target_compatible_with),
     deps = [
+        "//src/google/protobuf:descriptor_upb_reflection_proto",
         "//third_party/utf8_range",
         "//upb:base",
-        "//upb:descriptor_upb_proto_reflection",
         "//upb:eps_copy_input_stream",
         "//upb:message",
         "//upb:message_compare",
diff --git a/src/google/protobuf/BUILD.bazel b/src/google/protobuf/BUILD.bazel
index 5aa68d41f5..239e31890f 100644
--- a/src/google/protobuf/BUILD.bazel
+++ b/src/google/protobuf/BUILD.bazel
@@ -6,6 +6,9 @@ load("@rules_cc//cc:defs.bzl", "cc_library", "cc_test")
 load("@rules_pkg//pkg:mappings.bzl", "pkg_files", "strip_prefix")
 load("//bazel:cc_proto_library.bzl", "cc_proto_library")
 load("//bazel:proto_library.bzl", "proto_library")
+load("//bazel:upb_c_proto_library.bzl", "upb_c_proto_library")
+load("//bazel:upb_minitable_proto_library.bzl", "upb_minitable_proto_library")
+load("//bazel:upb_proto_reflection_library.bzl", "upb_proto_reflection_library")
 load("//build_defs:cpp_opts.bzl", "COPTS", "LINK_OPTS")
 load("//upb/cmake:build_defs.bzl", "staleness_test")
 
@@ -223,6 +226,24 @@ proto_library(
     ],
 )
 
+upb_c_proto_library(
+    name = "descriptor_upb_c_proto",
+    visibility = ["//:__subpackages__"],
+    deps = [":descriptor_proto"],
+)
+
+upb_minitable_proto_library(
+    name = "descriptor_upb_minitable_proto",
+    visibility = ["//:__subpackages__"],
+    deps = [":descriptor_proto"],
+)
+
+upb_proto_reflection_library(
+    name = "descriptor_upb_reflection_proto",
+    visibility = ["//:__subpackages__"],
+    deps = [":descriptor_proto"],
+)
+
 proto_library(
     name = "cpp_features_proto",
     srcs = ["cpp_features.proto"],
diff --git a/src/google/protobuf/compiler/BUILD.bazel b/src/google/protobuf/compiler/BUILD.bazel
index 0f4c0539cf..e9df8e4ffa 100644
--- a/src/google/protobuf/compiler/BUILD.bazel
+++ b/src/google/protobuf/compiler/BUILD.bazel
@@ -11,6 +11,8 @@ load(
 )
 load("//bazel:cc_proto_library.bzl", "cc_proto_library")
 load("//bazel:proto_library.bzl", "proto_library")
+load("//bazel:upb_c_proto_library.bzl", "upb_c_proto_library")
+load("//bazel:upb_proto_reflection_library.bzl", "upb_proto_reflection_library")
 load("//build_defs:arch_tests.bzl", "aarch64_test", "x86_64_test")
 load("//build_defs:cpp_opts.bzl", "COPTS")
 load("test_plugin_injection.bzl", "inject_plugin_paths")
@@ -32,6 +34,18 @@ cc_proto_library(
     deps = [":plugin_proto"],
 )
 
+upb_c_proto_library(
+    name = "plugin_upb_c_proto",
+    visibility = ["//upb_generator:__subpackages__"],
+    deps = [":plugin_proto"],
+)
+
+upb_proto_reflection_library(
+    name = "plugin_upb_reflection_proto",
+    visibility = ["//upb_generator:__subpackages__"],
+    deps = [":plugin_proto"],
+)
+
 cc_library(
     name = "importer",
     srcs = [
diff --git a/upb/BUILD b/upb/BUILD
index b46ee4b477..48de9628f2 100644
--- a/upb/BUILD
+++ b/upb/BUILD
@@ -261,7 +261,6 @@ upb_amalgamation(
     ],
     libs = [
         ":base",
-        ":descriptor_upb_minitable_proto",
         ":descriptor_upb_proto",
         ":eps_copy_input_stream",
         ":generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
@@ -276,6 +275,8 @@ upb_amalgamation(
         ":reflection",
         ":wire",
         ":wire_reader",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf:descriptor_upb_minitable_proto",
         "//upb/base:internal",
         "//upb/hash:hash",
         "//upb/lex:lex",
@@ -307,8 +308,6 @@ upb_amalgamation(
     ],
     libs = [
         ":base",
-        ":descriptor_upb_minitable_proto",
-        ":descriptor_upb_proto_reflection",
         ":descriptor_upb_proto",
         ":eps_copy_input_stream",
         ":generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
@@ -324,6 +323,9 @@ upb_amalgamation(
         ":reflection",
         ":wire",
         ":wire_reader",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf:descriptor_upb_minitable_proto",
+        "//src/google/protobuf:descriptor_upb_reflection_proto",
         "//upb/base:internal",
         "//upb/hash:hash",
         "//upb/lex:lex",
@@ -356,7 +358,6 @@ upb_amalgamation(
     ],
     libs = [
         ":base",
-        ":descriptor_upb_minitable_proto",
         ":descriptor_upb_proto",
         ":eps_copy_input_stream",
         ":generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
@@ -372,6 +373,8 @@ upb_amalgamation(
         ":reflection",
         ":wire",
         ":wire_reader",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf:descriptor_upb_minitable_proto",
         "//upb/base:internal",
         "//upb/hash:hash",
         "//upb/lex:lex",
diff --git a/upb/bazel/amalgamate.py b/upb/bazel/amalgamate.py
index f4e83fc79a..96f142c791 100755
--- a/upb/bazel/amalgamate.py
+++ b/upb/bazel/amalgamate.py
@@ -106,6 +106,8 @@ class Amalgamator:
     if include.endswith("hpp"):
       # Skip, we don't support the amalgamation from C++.
       return True
+    if re.search(r"stage\d/", include):
+      return True
     elif include in self.included:
       return True
     else:
diff --git a/upb/cmake/BUILD.bazel b/upb/cmake/BUILD.bazel
index fdf0f23226..81338ed327 100644
--- a/upb/cmake/BUILD.bazel
+++ b/upb/cmake/BUILD.bazel
@@ -47,8 +47,8 @@ genrule(
 genrule(
     name = "copy_protos",
     srcs = [
-        "//upb:descriptor_upb_proto",
-        "//upb:descriptor_upb_minitable_proto",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf:descriptor_upb_minitable_proto",
     ],
     outs = [
         "generated-in/google/protobuf/descriptor.upb.h",
diff --git a/upb/port/def.inc b/upb/port/def.inc
index 2bcdb884f9..efc6d5d40b 100644
--- a/upb/port/def.inc
+++ b/upb/port/def.inc
@@ -338,10 +338,11 @@ void __asan_unpoison_memory_region(void const volatile *addr, size_t size);
 // #define UPB_IS_GOOGLE3
 // end:google_only
 
-#if defined(UPB_IS_GOOGLE3) && !defined(UPB_BOOTSTRAP_STAGE0)
+#if defined(UPB_IS_GOOGLE3) && \
+    (!defined(UPB_BOOTSTRAP_STAGE) || UPB_BOOTSTRAP_STAGE != 0)
 #define UPB_DESC(sym) proto2_##sym
 #define UPB_DESC_MINITABLE(sym) &proto2__##sym##_msg_init
-#elif defined(UPB_BOOTSTRAP_STAGE0)
+#elif defined(UPB_BOOTSTRAP_STAGE) && UPB_BOOTSTRAP_STAGE == 0
 #define UPB_DESC(sym) google_protobuf_##sym
 #define UPB_DESC_MINITABLE(sym) google__protobuf__##sym##_msg_init()
 #else
diff --git a/upb/reflection/BUILD b/upb/reflection/BUILD
index 694b1f0118..1251b57ec9 100644
--- a/upb/reflection/BUILD
+++ b/upb/reflection/BUILD
@@ -29,9 +29,7 @@ load(
 
 bootstrap_upb_proto_library(
     name = "descriptor_upb_proto",
-    base_dir = "",
-    # TODO: Export 'net/proto2/proto/descriptor.upb.h' and remove "-layering_check".
-    features = ["-layering_check"],
+    bootstrap_hdr = "descriptor_bootstrap.h",
     google3_src_files = ["net/proto2/proto/descriptor.proto"],
     google3_src_rules = ["//net/proto2/proto:descriptor_proto_source"],
     oss_src_files = ["google/protobuf/descriptor.proto"],
diff --git a/upb/reflection/common.h b/upb/reflection/common.h
index ebe3282853..e2d5221c02 100644
--- a/upb/reflection/common.h
+++ b/upb/reflection/common.h
@@ -12,17 +12,7 @@
 #ifndef UPB_REFLECTION_COMMON_H_
 #define UPB_REFLECTION_COMMON_H_
 
-// begin:google_only
-// #ifndef UPB_BOOTSTRAP_STAGE0
-// #include "net/proto2/proto/descriptor.upb.h"
-// #else
-// #include "google/protobuf/descriptor.upb.h"
-// #endif
-// end:google_only
-
-// begin:github_only
-#include "google/protobuf/descriptor.upb.h"
-// end:github_only
+#include "upb/reflection/descriptor_bootstrap.h"  // IWYU pragma: export
 
 typedef enum {
   kUpb_Syntax_Proto2 = 2,
diff --git a/upb/reflection/descriptor_bootstrap.h b/upb/reflection/descriptor_bootstrap.h
new file mode 100644
index 0000000000..c0b760cfa1
--- /dev/null
+++ b/upb/reflection/descriptor_bootstrap.h
@@ -0,0 +1,19 @@
+#ifndef THIRD_PARTY_UPB_UPB_REFLECTION_DESCRIPTOR_BOOTSTRAP_H_
+#define THIRD_PARTY_UPB_UPB_REFLECTION_DESCRIPTOR_BOOTSTRAP_H_
+
+// IWYU pragma: begin_exports
+
+#if defined(UPB_BOOTSTRAP_STAGE) && UPB_BOOTSTRAP_STAGE == 0
+// This header is checked in.
+#include "upb/reflection/stage0/google/protobuf/descriptor.upb.h"
+#elif UPB_BOOTSTRAP_STAGE == 1
+// This header is generated at build time by the bootstrapping process.
+#include "upb/reflection/stage1/google/protobuf/descriptor.upb.h"
+#else
+// This is the normal header, generated by upb_c_proto_library().
+#include "google/protobuf/descriptor.upb.h"
+#endif
+
+// IWYU pragma: end_exports
+
+#endif  // THIRD_PARTY_UPB_UPB_REFLECTION_DESCRIPTOR_BOOTSTRAP_H_
diff --git a/upb/reflection/field_def.c b/upb/reflection/field_def.c
index 59f1b0ad6c..3ba3cba4bc 100644
--- a/upb/reflection/field_def.c
+++ b/upb/reflection/field_def.c
@@ -591,7 +591,7 @@ static bool _upb_FieldDef_InferLegacyFeatures(
   }
 
 // begin:google_only
-// #ifndef UPB_BOOTSTRAP_STAGE0
+// #if UPB_BOOTSTRAP_STAGE != 0
 //   if (syntax == kUpb_Syntax_Proto3 &&
 //       UPB_DESC(FieldOptions_has_enforce_utf8)(options) &&
 //       !UPB_DESC(FieldOptions_enforce_utf8)(options)) {
diff --git a/upb/reflection/stage0/google/protobuf/descriptor.upb.c b/upb/reflection/stage0/google/protobuf/descriptor.upb.c
index eb58624981..3f5c6734cd 100644
--- a/upb/reflection/stage0/google/protobuf/descriptor.upb.c
+++ b/upb/reflection/stage0/google/protobuf/descriptor.upb.c
@@ -1,6 +1,6 @@
 #include <stddef.h>
 #include "upb/generated_code_support.h"
-#include "google/protobuf/descriptor.upb.h"
+#include "upb/reflection/descriptor_bootstrap.h"
 
 static upb_Arena* upb_BootstrapArena() {
   static upb_Arena* arena = NULL;
diff --git a/upb/util/BUILD b/upb/util/BUILD
index fe7e6c07e0..40b1f63af7 100644
--- a/upb/util/BUILD
+++ b/upb/util/BUILD
@@ -18,8 +18,8 @@ cc_library(
     hdrs = ["def_to_proto.h"],
     visibility = ["//visibility:public"],
     deps = [
+        "//src/google/protobuf:descriptor_upb_c_proto",
         "//upb:base",
-        "//upb:descriptor_upb_proto",
         "//upb:port",
         "//upb:reflection",
         "//upb/reflection:internal",
@@ -52,9 +52,9 @@ cc_library(
     deps = [
         ":def_to_proto",
         "//:protobuf",
+        "//src/google/protobuf:descriptor_upb_c_proto",
         "//src/google/protobuf/util:differencer",
         "//upb:base",
-        "//upb:descriptor_upb_proto",
         "//upb:mem",
         "//upb/reflection:internal",
         "@com_google_googletest//:gtest",
@@ -72,10 +72,10 @@ cc_test(
         ":def_to_proto_test_upb_proto",
         ":def_to_proto_test_upb_proto_reflection",
         "//:protobuf",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf:descriptor_upb_reflection_proto",
         "//src/google/protobuf/util:differencer",
         "//upb:base",
-        "//upb:descriptor_upb_proto",
-        "//upb:descriptor_upb_proto_reflection",
         "//upb:mem",
         "//upb:reflection",
         "//upb/test:parse_text_proto",
diff --git a/upb_generator/BUILD b/upb_generator/BUILD
index 43be436b74..cff397481a 100644
--- a/upb_generator/BUILD
+++ b/upb_generator/BUILD
@@ -59,9 +59,7 @@ upb_minitable_proto_library(
 
 bootstrap_upb_proto_library(
     name = "plugin_upb_proto",
-    base_dir = "",
-    # TODO: Export 'net/proto2/proto/descriptor.upb.h' and remove "-layering_check".
-    features = ["-layering_check"],
+    bootstrap_hdr = "plugin_bootstrap.h",
     google3_src_files = [
         "net/proto2/compiler/proto/profile.proto",
         "third_party/protobuf/compiler/plugin.proto",
@@ -234,10 +232,10 @@ cc_library(
     deps = [
         ":code_generator_request_upb_proto",
         ":code_generator_request_upb_proto_reflection",
-        ":plugin_upb_proto",
-        ":plugin_upb_proto_reflection",
+        "//src/google/protobuf:descriptor_upb_c_proto",
+        "//src/google/protobuf/compiler:plugin_upb_c_proto",
+        "//src/google/protobuf/compiler:plugin_upb_reflection_proto",
         "//upb:base",
-        "//upb:descriptor_upb_proto",
         "//upb:json",
         "//upb:mem",
         "//upb:message",
@@ -281,6 +279,7 @@ bootstrap_cc_library(
         "//upb:mini_table",
         "//upb:port",
         "//upb:wire_reader",
+        "@com_google_absl//absl/base:core_headers",
         "@com_google_absl//absl/container:flat_hash_map",
         "@com_google_absl//absl/container:flat_hash_set",
         "@com_google_absl//absl/log:absl_check",
@@ -400,7 +399,7 @@ cc_library(
         ":common",
         ":file_layout",
         ":plugin",
-        "//upb:descriptor_upb_proto",
+        "//src/google/protobuf:descriptor_upb_c_proto",
         "//upb:reflection",
         "//upb/util:def_to_proto",
     ],
diff --git a/upb_generator/bootstrap_compiler.bzl b/upb_generator/bootstrap_compiler.bzl
index e92fbafe75..23b6fc0827 100644
--- a/upb_generator/bootstrap_compiler.bzl
+++ b/upb_generator/bootstrap_compiler.bzl
@@ -51,38 +51,38 @@ def bootstrap_cc_binary(name, deps = [], bootstrap_deps = [], **kwargs):
             **kwargs
         )
 
-def _generated_srcs_for_suffix(prefix, srcs, suffix):
-    return [prefix + "/" + src[:-len(".proto")] + suffix for src in srcs]
+def _generated_file(proto, stage, generator, suffix):
+    stripped = proto[:-len(".proto")]
+    return "{}/{}.{}.{}".format(stage, stripped, generator, suffix)
 
-def _generated_srcs_for_generator(prefix, srcs, generator):
-    ret = _generated_srcs_for_suffix(prefix, srcs, ".{}.h".format(generator))
+def _generated_files(protos, stage, generator, suffix):
+    return [_generated_file(proto, stage, generator, suffix) for proto in protos]
 
-    if generator != "upb" or prefix.endswith("stage0"):
-        ret += _generated_srcs_for_suffix(prefix, srcs, ".{}.c".format(generator))
+def _generated_hdrs_and_srcs(protos, stage, generator):
+    ret = _generated_files(protos, stage, generator, "h")
+    if generator != "upb" or stage == "stage0":
+        ret += _generated_files(protos, stage, generator, "c")
     return ret
 
-def _generated_srcs(prefix, srcs):
-    return _generated_srcs_for_generator(prefix, srcs, "upb")
-
-def _stage0_proto_staleness_test(name, base_dir, src_files, src_rules, strip_prefix):
+def _stage0_proto_staleness_test(name, src_files, src_rules, strip_prefix):
     native.genrule(
         name = name + "_generate_bootstrap",
         srcs = src_rules,
-        outs = _generated_srcs("bootstrap_generated_sources/" + base_dir + "stage0", src_files),
+        outs = ["bootstrap_generated_sources/" + f for f in _generated_hdrs_and_srcs(src_files, "stage0", "upb")],
         tools = [_protoc, _upbc("upb", 0)],
         cmd =
             "$(location " + _protoc + ") " +
             "-I$(GENDIR)/" + strip_prefix + " " + _extra_proto_path +
             "--plugin=protoc-gen-upb=$(location " + _upbc("upb", 0) + ") " +
-            "--upb_out=bootstrap_upb:$(@D)/bootstrap_generated_sources/" + base_dir + "stage0 " +
+            "--upb_out=bootstrap_stage=0:$(@D)/bootstrap_generated_sources/stage0 " +
             " ".join(src_files),
     )
 
     staleness_test(
         name = name + "_stage0_staleness_test",
-        outs = _generated_srcs(base_dir + "stage0", src_files),
+        outs = _generated_hdrs_and_srcs(src_files, "stage0", "upb"),
         generated_pattern = "bootstrap_generated_sources/%s",
-        target_files = native.glob([base_dir + "stage0/**"]),
+        target_files = native.glob(["stage0/**"]),
         # To avoid skew problems for descriptor.proto/pluging.proto between
         # GitHub repos.  It's not critical that the checked-in protos are up to
         # date for every change, they just needs to be complete enough to have
@@ -90,15 +90,15 @@ def _stage0_proto_staleness_test(name, base_dir, src_files, src_rules, strip_pre
         tags = ["manual"],
     )
 
-def _generate_stage1_proto(name, base_dir, src_files, src_rules, generator, kwargs):
+def _generate_stage1_proto(name, src_files, src_rules, generator, kwargs):
     native.genrule(
         name = "gen_{}_{}_stage1".format(name, generator),
         srcs = src_rules,
-        outs = _generated_srcs_for_generator(base_dir + "stage1", src_files, generator),
+        outs = _generated_hdrs_and_srcs(src_files, "stage1", generator),
         cmd = "$(location " + _protoc + ") " +
               "--plugin=protoc-gen-" + generator +
               "=$(location " + _upbc(generator, 0) + ") " + _extra_proto_path +
-              "--" + generator + "_out=$(RULEDIR)/" + base_dir + "stage1 " +
+              "--" + generator + "_out=bootstrap_stage=1:$(RULEDIR)/stage1 " +
               " ".join(src_files),
         visibility = ["//upb_generator:__pkg__"],
         tools = [
@@ -109,7 +109,7 @@ def _generate_stage1_proto(name, base_dir, src_files, src_rules, generator, kwar
     )
 
 # begin:github_only
-def _cmake_staleness_test(name, base_dir, src_files, proto_lib_deps, **kwargs):
+def _cmake_staleness_test(name, src_files, proto_lib_deps, **kwargs):
     upb_minitable_proto_library(
         name = name + "_minitable",
         deps = proto_lib_deps,
@@ -117,15 +117,15 @@ def _cmake_staleness_test(name, base_dir, src_files, proto_lib_deps, **kwargs):
     )
 
     # Copy the final gencode for staleness comparison
-    files = _generated_srcs("cmake" + base_dir, src_files) + \
-            _generated_srcs_for_generator("cmake" + base_dir, src_files, "upb_minitable")
+    files = _generated_hdrs_and_srcs(src_files, "cmake", "upb") + \
+            _generated_hdrs_and_srcs(src_files, "cmake", "upb_minitable")
     genrule = 0
     for src in files:
         genrule += 1
         native.genrule(
             name = name + "_copy_gencode_%d" % genrule,
             outs = ["generated_sources/" + src],
-            srcs = [name, name + "_minitable"],
+            srcs = [name + "_upb_proto", name + "_minitable"],
             cmd = """
                 mkdir -p $(@D)
                 for src in $(SRCS); do
@@ -148,7 +148,7 @@ def _cmake_staleness_test(name, base_dir, src_files, proto_lib_deps, **kwargs):
 
 def bootstrap_upb_proto_library(
         name,
-        base_dir,
+        bootstrap_hdr,
         google3_src_files,
         google3_src_rules,
         oss_src_files,
@@ -162,7 +162,6 @@ def bootstrap_upb_proto_library(
 
     Args:
         name: Name of this rule.  This name will resolve to a upb_proto_library().
-        base_dir: The directory that all generated files should be placed under.
         google3_src_files: Google3 filenames of .proto files that should be built by this rule.
           The names should be relative to the depot base.
         google3_src_rules: Target names of the Blaze rules that will provide these filenames.
@@ -177,17 +176,15 @@ def bootstrap_upb_proto_library(
         **kwargs: Other arguments that will be passed through to cc_library(), genrule(), and
           upb_proto_library().
     """
-    _stage0_proto_staleness_test(name, base_dir, oss_src_files, oss_src_rules, oss_strip_prefix)
+    _stage0_proto_staleness_test(name, oss_src_files, oss_src_rules, oss_strip_prefix)
 
     # stage0 uses checked-in protos, and has no MiniTable.
     native.cc_library(
         name = name + "_stage0",
-        srcs = _generated_srcs_for_suffix(base_dir + "stage0", oss_src_files, ".upb.c"),
-        hdrs = _generated_srcs_for_suffix(base_dir + "stage0", oss_src_files, ".upb.h"),
-        includes = [base_dir + "stage0"],
+        srcs = _generated_hdrs_and_srcs(oss_src_files, "stage0", "upb"),
+        hdrs = [bootstrap_hdr],
         visibility = ["//upb_generator:__pkg__"],
-        # This macro signals to the runtime that it must use OSS APIs for descriptor.proto/plugin.proto.
-        defines = ["UPB_BOOTSTRAP_STAGE0"],
+        defines = ["UPB_BOOTSTRAP_STAGE=0"],
         deps = [
             "//upb:generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
             "//upb:mini_table",
@@ -199,41 +196,48 @@ def bootstrap_upb_proto_library(
     src_rules = google3_src_rules if _is_google3 else oss_src_rules
 
     # Generate stage1 protos (C API and MiniTables) using stage0 compiler.
-    _generate_stage1_proto(name, base_dir, src_files, src_rules, "upb", kwargs)
-    _generate_stage1_proto(name, base_dir, src_files, src_rules, "upb_minitable", kwargs)
+    _generate_stage1_proto(name, src_files, src_rules, "upb", kwargs)
+    _generate_stage1_proto(name, src_files, src_rules, "upb_minitable", kwargs)
 
     native.cc_library(
         name = name + "_minitable_stage1",
-        srcs = _generated_srcs_for_suffix(base_dir + "stage1", src_files, ".upb_minitable.c"),
-        hdrs = _generated_srcs_for_suffix(base_dir + "stage1", src_files, ".upb_minitable.h"),
-        includes = [base_dir + "stage1"],
+        srcs = _generated_files(src_files, "stage1", "upb_minitable", "c"),
+        hdrs = _generated_files(src_files, "stage1", "upb_minitable", "h"),
         visibility = ["//upb_generator:__pkg__"],
+        defines = ["UPB_BOOTSTRAP_STAGE=1"],
         deps = [
             "//upb:generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
-        ] + [dep + "_stage1" for dep in deps],
+        ] + [dep + "_minitable_stage1" for dep in deps],
         **kwargs
     )
     native.cc_library(
         name = name + "_stage1",
-        hdrs = _generated_srcs_for_suffix(base_dir + "stage1", src_files, ".upb.h"),
-        includes = [base_dir + "stage1"],
+        srcs = _generated_files(src_files, "stage1", "upb", "h"),
+        hdrs = [bootstrap_hdr],
         visibility = ["//upb_generator:__pkg__"],
+        defines = ["UPB_BOOTSTRAP_STAGE=1"],
         deps = [
             "//upb:generated_code_support__only_for_generated_code_do_not_use__i_give_permission_to_break_me",
             ":" + name + "_minitable_stage1",
-        ] + [dep + "_stage1" for dep in deps],
+        ] + [dep + "_minitable_stage1" for dep in deps],
         **kwargs
     )
 
     # The final protos are generated via normal upb_proto_library().
     upb_proto_library(
-        name = name,
+        name = name + "_upb_proto",
         deps = proto_lib_deps,
+        **kwargs
+    )
+    native.cc_library(
+        name = name,
+        hdrs = [bootstrap_hdr],
+        deps = [name + "_upb_proto"],
         visibility = visibility,
         **kwargs
     )
 
     # begin:github_only
-    _cmake_staleness_test(name, base_dir, src_files, proto_lib_deps, **kwargs)
+    _cmake_staleness_test(name, src_files, proto_lib_deps, **kwargs)
 
 # end:github_only
diff --git a/upb_generator/common.cc b/upb_generator/common.cc
index 2dbe9d7f78..ef2038323c 100644
--- a/upb_generator/common.cc
+++ b/upb_generator/common.cc
@@ -75,12 +75,36 @@ std::string FileLayoutName(upb::FileDefPtr file) {
   return ToCIdent(file.name()) + "_upb_file_layout";
 }
 
-std::string CApiHeaderFilename(upb::FileDefPtr file) {
+bool HasFilename(upb::FileDefPtr file, absl::string_view filename) {
+  return file.name() == filename;
+}
+
+bool IsDescriptorProto(upb::FileDefPtr file) {
+  return HasFilename(file, "net/proto2/proto/descriptor.proto") ||
+         HasFilename(file, "google/protobuf/descriptor.proto");
+}
+
+std::string CApiHeaderFilename(upb::FileDefPtr file, bool bootstrap) {
+  if (bootstrap) {
+    if (IsDescriptorProto(file)) {
+      return "upb/reflection/descriptor_bootstrap.h";
+    } else {
+      return "upb_generator/plugin_bootstrap.h";
+    }
+  }
   return StripExtension(file.name()) + ".upb.h";
 }
 
-std::string MiniTableHeaderFilename(upb::FileDefPtr file) {
-  return StripExtension(file.name()) + ".upb_minitable.h";
+std::string MiniTableHeaderFilename(upb::FileDefPtr file, bool bootstrap) {
+  std::string base;
+  if (bootstrap) {
+    if (IsDescriptorProto(file)) {
+      base = "upb/reflection/stage1/";
+    } else {
+      base = "upb_generator/stage1/";
+    }
+  }
+  return base + StripExtension(file.name()) + ".upb_minitable.h";
 }
 
 std::string EnumInit(upb::EnumDefPtr descriptor) {
diff --git a/upb_generator/common.h b/upb_generator/common.h
index 2afa005d9f..415fa2296f 100644
--- a/upb_generator/common.h
+++ b/upb_generator/common.h
@@ -66,8 +66,8 @@ PROTOC_EXPORT std::string MessageInit(absl::string_view full_name);
 std::string MessageInitName(upb::MessageDefPtr descriptor);
 std::string MessageName(upb::MessageDefPtr descriptor);
 std::string FileLayoutName(upb::FileDefPtr file);
-std::string MiniTableHeaderFilename(upb::FileDefPtr file);
-std::string CApiHeaderFilename(upb::FileDefPtr file);
+std::string MiniTableHeaderFilename(upb::FileDefPtr file, bool bootstrap);
+std::string CApiHeaderFilename(upb::FileDefPtr file, bool bootstrap);
 std::string PadPrefix(absl::string_view tag);
 
 std::string EnumInit(upb::EnumDefPtr descriptor);
diff --git a/upb_generator/file_layout.h b/upb_generator/file_layout.h
index a2aad3339a..4bf832e124 100644
--- a/upb_generator/file_layout.h
+++ b/upb_generator/file_layout.h
@@ -9,24 +9,14 @@
 #define UPB_GENERATOR_FILE_LAYOUT_H
 
 #include <string>
-
-// begin:google_only
-// #ifndef UPB_BOOTSTRAP_STAGE0
-// #include "google/protobuf/descriptor.upb.h"
-// #else
-// #include "google/protobuf/descriptor.upb.h"
-// #endif
-// end:google_only
-
-// begin:github_only
-#include "google/protobuf/descriptor.upb.h"
-// end:github_only
+#include <vector>
 
 #include "absl/container/flat_hash_map.h"
 #include "upb/base/status.hpp"
 #include "upb/mini_descriptor/decode.h"
 #include "upb/reflection/def.h"
 #include "upb/reflection/def.hpp"
+#include "upb/reflection/descriptor_bootstrap.h"
 
 // Must be last
 #include "upb/port/def.inc"
diff --git a/upb_generator/plugin.h b/upb_generator/plugin.h
index 31ca530ae3..b5edda151f 100644
--- a/upb_generator/plugin.h
+++ b/upb_generator/plugin.h
@@ -17,26 +17,13 @@
 #include <io.h>
 #endif
 
-// begin:google_only
-// #ifndef UPB_BOOTSTRAP_STAGE0
-// #include "google/protobuf/descriptor.upb.h"
-// #include "google/protobuf/compiler/plugin.upb.h"
-// #else
-// #include "google/protobuf/compiler/plugin.upb.h"
-// #include "google/protobuf/descriptor.upb.h"
-// #endif
-// end:google_only
-
-// begin:github_only
-#include "google/protobuf/compiler/plugin.upb.h"
-#include "google/protobuf/descriptor.upb.h"
-// end:github_only
-
 #include "absl/container/flat_hash_set.h"
 #include "absl/log/absl_log.h"
 #include "absl/strings/str_split.h"
 #include "absl/strings/string_view.h"
 #include "upb/reflection/def.hpp"
+#include "upb/reflection/descriptor_bootstrap.h"
+#include "upb_generator/plugin_bootstrap.h"
 
 // Must be last.
 #include "upb/port/def.inc"
diff --git a/upb_generator/plugin_bootstrap.h b/upb_generator/plugin_bootstrap.h
new file mode 100644
index 0000000000..87afc06fbb
--- /dev/null
+++ b/upb_generator/plugin_bootstrap.h
@@ -0,0 +1,19 @@
+#ifndef THIRD_PARTY_UPB_UPB_GENERATOR_PLUGIN_BOOTSTRAP_H_
+#define THIRD_PARTY_UPB_UPB_GENERATOR_PLUGIN_BOOTSTRAP_H_
+
+// IWYU pragma: begin_exports
+
+#if defined(UPB_BOOTSTRAP_STAGE) && UPB_BOOTSTRAP_STAGE == 0
+// This header is checked in.
+#include "upb_generator/stage0/google/protobuf/compiler/plugin.upb.h"
+#elif UPB_BOOTSTRAP_STAGE == 1
+// This header is generated at build time by the bootstrapping process.
+#include "upb_generator/stage1/google/protobuf/compiler/plugin.upb.h"
+#else
+// This is the normal header, generated by upb_c_proto_library().
+#include "google/protobuf/compiler/plugin.upb.h"
+#endif
+
+// IWYU pragma: end_exports
+
+#endif  // THIRD_PARTY_UPB_UPB_GENERATOR_PLUGIN_BOOTSTRAP_H_
diff --git a/upb_generator/protoc-gen-upb.cc b/upb_generator/protoc-gen-upb.cc
index 10b51f0dfa..16ea022c9d 100644
--- a/upb_generator/protoc-gen-upb.cc
+++ b/upb_generator/protoc-gen-upb.cc
@@ -6,6 +6,7 @@
 // https://developers.google.com/open-source/licenses/bsd
 
 #include <algorithm>
+#include <cassert>
 #include <cmath>
 #include <cstddef>
 #include <cstdint>
@@ -17,10 +18,12 @@
 #include <utility>
 #include <vector>
 
+#include "absl/base/macros.h"
 #include "absl/log/absl_check.h"
 #include "absl/log/absl_log.h"
 #include "absl/strings/escaping.h"
 #include "absl/strings/match.h"
+#include "absl/strings/numbers.h"
 #include "absl/strings/str_cat.h"
 #include "absl/strings/str_replace.h"
 #include "absl/strings/string_view.h"
@@ -31,7 +34,6 @@
 #include "upb/base/string_view.h"
 #include "upb/mini_table/field.h"
 #include "upb/reflection/def.hpp"
-#include "upb/wire/types.h"
 #include "upb_generator/common.h"
 #include "upb_generator/file_layout.h"
 #include "upb_generator/names.h"
@@ -45,7 +47,7 @@ namespace generator {
 namespace {
 
 struct Options {
-  bool bootstrap = false;
+  int bootstrap_stage = -1;  // -1 means not bootstrapped.
   bool strip_nonfunctional_codegen = false;
 };
 
@@ -55,7 +57,7 @@ std::string SourceFilename(upb::FileDefPtr file) {
 
 std::string MessageMiniTableRef(upb::MessageDefPtr descriptor,
                                 const Options& options) {
-  if (options.bootstrap) {
+  if (options.bootstrap_stage == 0) {
     return absl::StrCat(MessageInitName(descriptor), "()");
   } else {
     return absl::StrCat("&", MessageInitName(descriptor));
@@ -68,7 +70,7 @@ std::string EnumInitName(upb::EnumDefPtr descriptor) {
 
 std::string EnumMiniTableRef(upb::EnumDefPtr descriptor,
                              const Options& options) {
-  if (options.bootstrap) {
+  if (options.bootstrap_stage == 0) {
     return absl::StrCat(EnumInitName(descriptor), "()");
   } else {
     return absl::StrCat("&", EnumInitName(descriptor));
@@ -887,21 +889,26 @@ void WriteHeader(const DefPoolPair& pools, upb::FileDefPtr file,
     if (i == 0) {
       output("/* Public Imports. */\n");
     }
-    output("#include \"$0\"\n", CApiHeaderFilename(file.public_dependency(i)));
+    output("#include \"$0\"\n",
+           CApiHeaderFilename(file.public_dependency(i),
+                              options.bootstrap_stage >= 0));
   }
   if (file.public_dependency_count() > 0) {
     output("\n");
   }
 
-  if (!options.bootstrap) {
-    output("#include \"$0\"\n\n", MiniTableHeaderFilename(file));
+  if (options.bootstrap_stage != 0) {
+    output("#include \"$0\"\n\n",
+           MiniTableHeaderFilename(file, options.bootstrap_stage >= 0));
     for (int i = 0; i < file.dependency_count(); i++) {
       if (options.strip_nonfunctional_codegen &&
           google::protobuf::compiler::IsKnownFeatureProto(file.dependency(i).name())) {
         // Strip feature imports for editions codegen tests.
         continue;
       }
-      output("#include \"$0\"\n", MiniTableHeaderFilename(file.dependency(i)));
+      output("#include \"$0\"\n",
+             MiniTableHeaderFilename(file.dependency(i),
+                                     options.bootstrap_stage >= 0));
     }
     output("\n");
   }
@@ -915,7 +922,7 @@ void WriteHeader(const DefPoolPair& pools, upb::FileDefPtr file,
       "#endif\n"
       "\n");
 
-  if (options.bootstrap) {
+  if (options.bootstrap_stage == 0) {
     for (auto message : this_file_messages) {
       output("extern const upb_MiniTable* $0();\n", MessageInitName(message));
     }
@@ -1005,7 +1012,7 @@ std::string FieldInitializer(upb::FieldDefPtr field,
                              const upb_MiniTableField* field64,
                              const upb_MiniTableField* field32,
                              const Options& options) {
-  if (options.bootstrap) {
+  if (options.bootstrap_stage == 0) {
     ABSL_CHECK(!field.is_extension());
     return absl::Substitute(
         "*upb_MiniTable_FindFieldByNumber($0, $1)",
@@ -1034,7 +1041,7 @@ std::string FieldInitializerStrong(const DefPoolPair& pools,
                                    upb::FieldDefPtr field,
                                    const Options& options) {
   std::string ret = FieldInitializer(pools, field, options);
-  if (!options.bootstrap && field.IsSubMessage()) {
+  if (options.bootstrap_stage != 0 && field.IsSubMessage()) {
     ret += ";\n" + StrongReference(field);
   }
   return ret;
@@ -1109,14 +1116,16 @@ void WriteMiniDescriptorSource(const DefPoolPair& pools, upb::FileDefPtr file,
       "#include <stddef.h>\n"
       "#include \"upb/generated_code_support.h\"\n"
       "#include \"$0\"\n\n",
-      CApiHeaderFilename(file));
+      CApiHeaderFilename(file, options.bootstrap_stage >= 0));
 
   for (int i = 0; i < file.dependency_count(); i++) {
     if (options.strip_nonfunctional_codegen &&
         google::protobuf::compiler::IsKnownFeatureProto(file.dependency(i).name())) {
       continue;
     }
-    output("#include \"$0\"\n", CApiHeaderFilename(file.dependency(i)));
+    output(
+        "#include \"$0\"\n",
+        CApiHeaderFilename(file.dependency(i), options.bootstrap_stage >= 0));
   }
 
   output(
@@ -1143,9 +1152,9 @@ void GenerateFile(const DefPoolPair& pools, upb::FileDefPtr file,
                   const Options& options, Plugin* plugin) {
   Output h_output;
   WriteHeader(pools, file, options, h_output);
-  plugin->AddOutputFile(CApiHeaderFilename(file), h_output.output());
+  plugin->AddOutputFile(CApiHeaderFilename(file, false), h_output.output());
 
-  if (options.bootstrap) {
+  if (options.bootstrap_stage == 0) {
     Output c_output;
     WriteMiniDescriptorSource(pools, file, options, c_output);
     plugin->AddOutputFile(SourceFilename(file), c_output.output());
@@ -1161,8 +1170,11 @@ void GenerateFile(const DefPoolPair& pools, upb::FileDefPtr file,
 
 bool ParseOptions(Plugin* plugin, Options* options) {
   for (const auto& pair : ParseGeneratorParameter(plugin->parameter())) {
-    if (pair.first == "bootstrap_upb") {
-      options->bootstrap = true;
+    if (pair.first == "bootstrap_stage") {
+      if (!absl::SimpleAtoi(pair.second, &options->bootstrap_stage)) {
+        plugin->SetError(absl::Substitute("Bad stage: $0", pair.second));
+        return false;
+      }
     } else if (pair.first == "experimental_strip_nonfunctional_codegen") {
       options->strip_nonfunctional_codegen = true;
     } else {
diff --git a/upb_generator/protoc-gen-upb_minitable-main.cc b/upb_generator/protoc-gen-upb_minitable-main.cc
index 2073f077ff..f970235ba1 100644
--- a/upb_generator/protoc-gen-upb_minitable-main.cc
+++ b/upb_generator/protoc-gen-upb_minitable-main.cc
@@ -35,8 +35,9 @@ absl::string_view ToStringView(upb_StringView str) {
 void GenerateFile(const DefPoolPair& pools, upb::FileDefPtr file,
                   const MiniTableOptions& options, Plugin* plugin) {
   Output h_output;
-  WriteMiniTableHeader(pools, file, h_output);
-  plugin->AddOutputFile(MiniTableHeaderFilename(file), h_output.output());
+  WriteMiniTableHeader(pools, file, options, h_output);
+  plugin->AddOutputFile(MiniTableHeaderFilename(file, false),
+                        h_output.output());
 
   Output c_output;
   WriteMiniTableSource(pools, file, options, c_output);
@@ -49,7 +50,9 @@ void GenerateFile(const DefPoolPair& pools, upb::FileDefPtr file,
 
 bool ParseOptions(MiniTableOptions* options, Plugin* plugin) {
   for (const auto& pair : ParseGeneratorParameter(plugin->parameter())) {
-    if (pair.first == "experimental_strip_nonfunctional_codegen") {
+    if (pair.first == "bootstrap_stage") {
+      options->bootstrap = true;
+    } else if (pair.first == "experimental_strip_nonfunctional_codegen") {
       options->strip_nonfunctional_codegen = true;
     } else if (pair.first == "one_output_per_message") {
       options->one_output_per_message = true;
diff --git a/upb_generator/protoc-gen-upb_minitable.cc b/upb_generator/protoc-gen-upb_minitable.cc
index 333ab2ebd1..a12f0cdc97 100644
--- a/upb_generator/protoc-gen-upb_minitable.cc
+++ b/upb_generator/protoc-gen-upb_minitable.cc
@@ -488,7 +488,7 @@ void WriteExtension(const DefPoolPair& pools, upb::FieldDefPtr ext,
 }  // namespace
 
 void WriteMiniTableHeader(const DefPoolPair& pools, upb::FileDefPtr file,
-                          Output& output) {
+                          const MiniTableOptions& options, Output& output) {
   EmitFileWarning(file.name(), output);
   output(
       "#ifndef $0_UPB_MINITABLE_H_\n"
@@ -500,8 +500,9 @@ void WriteMiniTableHeader(const DefPoolPair& pools, upb::FileDefPtr file,
     if (i == 0) {
       output("/* Public Imports. */\n");
     }
-    output("#include \"$0\"\n",
-           MiniTableHeaderFilename(file.public_dependency(i)));
+    output(
+        "#include \"$0\"\n",
+        MiniTableHeaderFilename(file.public_dependency(i), options.bootstrap));
     if (i == file.public_dependency_count() - 1) {
       output("\n");
     }
@@ -560,7 +561,7 @@ void WriteMiniTableSourceIncludes(upb::FileDefPtr file,
       "#include <stddef.h>\n"
       "#include \"upb/generated_code_support.h\"\n"
       "#include \"$0\"\n",
-      MiniTableHeaderFilename(file));
+      MiniTableHeaderFilename(file, options.bootstrap));
 
   for (int i = 0; i < file.dependency_count(); i++) {
     if (options.strip_nonfunctional_codegen &&
@@ -568,7 +569,8 @@ void WriteMiniTableSourceIncludes(upb::FileDefPtr file,
       // Strip feature imports for editions codegen tests.
       continue;
     }
-    output("#include \"$0\"\n", MiniTableHeaderFilename(file.dependency(i)));
+    output("#include \"$0\"\n",
+           MiniTableHeaderFilename(file.dependency(i), options.bootstrap));
   }
 
   output(
diff --git a/upb_generator/protoc-gen-upb_minitable.h b/upb_generator/protoc-gen-upb_minitable.h
index 5023771ea0..358a157d7f 100644
--- a/upb_generator/protoc-gen-upb_minitable.h
+++ b/upb_generator/protoc-gen-upb_minitable.h
@@ -25,6 +25,7 @@ namespace upb {
 namespace generator {
 
 struct MiniTableOptions {
+  bool bootstrap = false;
   bool one_output_per_message = false;
   bool strip_nonfunctional_codegen = false;
 };
@@ -36,7 +37,7 @@ void WriteMiniTableMultipleSources(const DefPoolPair& pools,
                                    const MiniTableOptions& options,
                                    Plugin* plugin);
 void WriteMiniTableHeader(const DefPoolPair& pools, upb::FileDefPtr file,
-                          Output& output);
+                          const MiniTableOptions& options, Output& output);
 
 }  // namespace generator
 }  // namespace upb
diff --git a/upb_generator/protoc-gen-upbdefs.cc b/upb_generator/protoc-gen-upbdefs.cc
index ac1b3e4d59..e2742a5dc9 100644
--- a/upb_generator/protoc-gen-upbdefs.cc
+++ b/upb_generator/protoc-gen-upbdefs.cc
@@ -84,7 +84,7 @@ void WriteDefSource(upb::FileDefPtr file, const Options& options,
 
   output("#include \"upb/reflection/def.h\"\n");
   output("#include \"$0\"\n", DefHeaderFilename(file));
-  output("#include \"$0\"\n", MiniTableHeaderFilename(file));
+  output("#include \"$0\"\n", MiniTableHeaderFilename(file, false));
   output("\n");
 
   for (int i = 0; i < file.dependency_count(); i++) {
diff --git a/upb_generator/stage0/google/protobuf/compiler/plugin.upb.c b/upb_generator/stage0/google/protobuf/compiler/plugin.upb.c
index c1de6bd858..ae9abc87fa 100644
--- a/upb_generator/stage0/google/protobuf/compiler/plugin.upb.c
+++ b/upb_generator/stage0/google/protobuf/compiler/plugin.upb.c
@@ -1,8 +1,8 @@
 #include <stddef.h>
 #include "upb/generated_code_support.h"
-#include "google/protobuf/compiler/plugin.upb.h"
+#include "upb_generator/plugin_bootstrap.h"
 
-#include "google/protobuf/descriptor.upb.h"
+#include "upb/reflection/descriptor_bootstrap.h"
 static upb_Arena* upb_BootstrapArena() {
   static upb_Arena* arena = NULL;
   if (!arena) arena = upb_Arena_New();