diff --git a/cross/ubuntu-armhf.txt b/cross/ubuntu-armhf.txt
index 69e0c8611..aa75cdc59 100644
--- a/cross/ubuntu-armhf.txt
+++ b/cross/ubuntu-armhf.txt
@@ -14,6 +14,9 @@ ld = '/usr/bin/arm-linux/gnueabihf-ld'
 c_args = ['-DMESON_TEST_ISSUE_1665=1']
 cpp_args = '-DMESON_TEST_ISSUE_1665=1'
 
+[zlib:built-in options]
+c_std = 'c99'
+
 [properties]
 root = '/usr/arm-linux-gnueabihf'
 
diff --git a/mesonbuild/environment.py b/mesonbuild/environment.py
index 3a198e969..cb05b1d99 100644
--- a/mesonbuild/environment.py
+++ b/mesonbuild/environment.py
@@ -783,6 +783,21 @@ class Environment:
         self.wrap_resolver = None
         self.overrides = OptionOverrides()
         self.init_overrides()
+        self.check_dual_overrides()
+
+    def has_per_subproject_options(self):
+        for o in self.options:
+            if o.subproject:
+                return True
+        return False
+
+    def check_dual_overrides(self):
+        if self.has_per_subproject_options() and self.coredata.options[mesonlib.OptionKey('override_file')].value:
+            raise MesonException('''Tried to define a per-subproject option in a machine file when override_file was defined.
+This is not supported. All per-subproject options should be transitioned to
+use the override file. Machine file overrides are deprecatd and will be
+removed in a future Meson release.''')
+
 
     def _load_machine_file_options(self, config: 'ConfigParser', properties: Properties, machine: MachineChoice) -> None:
         """Read the contents of a Machine file and put it in the options store."""
@@ -814,6 +829,8 @@ class Environment:
                 subproject, section = section.split(':')
             else:
                 subproject = ''
+            if subproject != '':
+                mlog.deprecation('Per-subproject option values in machine files are deprecated, transition to using an override_file instead.')
             if section == 'built-in options':
                 for k, v in values.items():
                     key = OptionKey.from_string(k)
diff --git a/mesonbuild/msetup.py b/mesonbuild/msetup.py
index b34894876..26d213458 100644
--- a/mesonbuild/msetup.py
+++ b/mesonbuild/msetup.py
@@ -224,6 +224,7 @@ class MesonApp:
         except Exception as e:
             mintro.write_meson_info_file(b, [e])
             raise
+        env.check_dual_overrides()
         # Print all default option values that don't match the current value
         for def_opt_name, def_opt_value, cur_opt_value in intr.get_non_matching_default_options():
             mlog.log('Option', mlog.bold(def_opt_name), 'is:',