diff --git a/tools/dep_updaters/update-base64.sh b/tools/dep_updaters/update-base64.sh
index b0d8693f82f1b7..5d10a205f881c2 100755
--- a/tools/dep_updaters/update-base64.sh
+++ b/tools/dep_updaters/update-base64.sh
@@ -51,6 +51,10 @@ mv "$WORKSPACE/base64" "$DEPS_DIR/base64/"
 # to work, we create it and leave it empty.
 echo "// Intentionally empty" >> "$DEPS_DIR/base64/base64/lib/config.h"
 
+# Clear out .gitconfig, otherwise config.h is ignored. That's dangerous when
+# people check in our tarballs into source control and run `git clean`.
+echo "# Intentionally empty" >> "$DEPS_DIR/base64/base64/.gitconfig"
+
 echo "All done!"
 echo ""
 echo "Please git add base64/base64, commit the new version:"