diff --git a/mesonbuild/mesonlib.py b/mesonbuild/mesonlib.py
index 59d4f8108..98c2366d6 100644
--- a/mesonbuild/mesonlib.py
+++ b/mesonbuild/mesonlib.py
@@ -1116,6 +1116,22 @@ def windows_proof_rmtree(f):
     shutil.rmtree(f)
 
 
+def windows_proof_rm(fpath):
+    """Like windows_proof_rmtree, but for a single file."""
+    if os.path.isfile(fpath):
+        os.chmod(fpath, os.stat(fpath).st_mode | stat.S_IWRITE | stat.S_IREAD)
+    delays = [0.1, 0.1, 0.2, 0.2, 0.2, 0.5, 0.5, 1, 1, 1, 1, 2]
+    for d in delays:
+        try:
+            os.unlink(fpath)
+            return
+        except FileNotFoundError:
+            return
+        except (OSError, PermissionError):
+            time.sleep(d)
+    os.unlink(fpath)
+
+
 def detect_subprojects(spdir_name, current_dir='', result=None):
     if result is None:
         result = {}
diff --git a/mesonbuild/msetup.py b/mesonbuild/msetup.py
index 63014f196..56a0e9a79 100644
--- a/mesonbuild/msetup.py
+++ b/mesonbuild/msetup.py
@@ -73,7 +73,15 @@ class MesonApp:
             coredata.read_cmd_line_file(self.build_dir, options)
 
             try:
-                mesonlib.windows_proof_rmtree(self.build_dir)
+                # Don't delete the whole tree, just all of the files and
+                # folders in the tree. Otherwise calling wipe form the builddir
+                # will cause a crash
+                for l in os.listdir(self.build_dir):
+                    l = os.path.join(self.build_dir, l)
+                    if os.path.isdir(l):
+                        mesonlib.windows_proof_rmtree(l)
+                    else:
+                        mesonlib.windows_proof_rm(l)
             finally:
                 # Restore the file
                 path = os.path.dirname(filename)
diff --git a/run_unittests.py b/run_unittests.py
index 743eb12d3..6a1f5df9e 100755
--- a/run_unittests.py
+++ b/run_unittests.py
@@ -2922,11 +2922,7 @@ recommended as it is not supported on some platforms''')
         self.wipe()
         self.init(testdir, extra_args=['-Dstart_native=true'])
 
-    def test_reconfigure(self):
-        testdir = os.path.join(self.unit_test_dir, '46 reconfigure')
-        self.init(testdir, extra_args=['-Dopt1=val1'])
-        self.setconf('-Dopt2=val2')
-
+    def __reconfigure(self):
         # Set an older version to force a reconfigure from scratch
         filename = os.path.join(self.privatedir, 'coredata.dat')
         with open(filename, 'rb') as f:
@@ -2935,6 +2931,13 @@ recommended as it is not supported on some platforms''')
         with open(filename, 'wb') as f:
             pickle.dump(obj, f)
 
+    def test_reconfigure(self):
+        testdir = os.path.join(self.unit_test_dir, '46 reconfigure')
+        self.init(testdir, extra_args=['-Dopt1=val1'])
+        self.setconf('-Dopt2=val2')
+
+        self.__reconfigure()
+
         out = self.init(testdir, extra_args=['--reconfigure', '-Dopt3=val3'])
         self.assertRegex(out, 'WARNING:.*Regenerating configuration from scratch')
         self.assertRegex(out, 'opt1 val1')
@@ -2957,6 +2960,14 @@ recommended as it is not supported on some platforms''')
         self.build()
         self.run_tests()
 
+    def test_wipe_from_builddir(self):
+        testdir = os.path.join(self.common_test_dir, '162 custom target subdir depend files')
+        self.init(testdir)
+        self.__reconfigure()
+
+        with Path(self.builddir):
+            self.init(testdir, extra_args=['--wipe'])
+
     def test_target_construct_id_from_path(self):
         # This id is stable but not guessable.
         # The test is supposed to prevent unintentional