diff --git a/upb_generator/bootstrap_compiler.bzl b/upb_generator/bootstrap_compiler.bzl
index 4a3bd8ccdd02..e92fbafe75a0 100644
--- a/upb_generator/bootstrap_compiler.bzl
+++ b/upb_generator/bootstrap_compiler.bzl
@@ -126,7 +126,14 @@ def _cmake_staleness_test(name, base_dir, src_files, proto_lib_deps, **kwargs):
             name = name + "_copy_gencode_%d" % genrule,
             outs = ["generated_sources/" + src],
             srcs = [name, name + "_minitable"],
-            cmd = "mkdir -p $(@D); for src in $(SRCS); do cp -f $$src $(@D) || echo 'copy failed!'; done",
+            cmd = """
+                mkdir -p $(@D)
+                for src in $(SRCS); do
+                    if [[ $$src == *%s ]]; then
+                        cp -f $$src $(@D) || echo 'copy failed!'
+                    fi
+                done
+            """ % src[src.rfind("/"):],
         )
 
     # Keep bazel gencode in sync with our checked-in sources needed for cmake builds.