diff --git a/pyodide_build/buildpkg.py b/pyodide_build/buildpkg.py
index 6ad323b..9e650a6 100755
--- a/pyodide_build/buildpkg.py
+++ b/pyodide_build/buildpkg.py
@@ -11,7 +11,6 @@
 import shutil
 import subprocess
 import sys
-import warnings
 from collections.abc import Iterator
 from datetime import datetime
 from pathlib import Path
@@ -349,12 +348,18 @@ def _download_and_extract(self) -> None:
             shutil.copy(tarballpath, self.src_dist_dir)
             return
 
-        with warnings.catch_warnings():
-            # Python 3.12-3.13 emits a DeprecationWarning when using shutil.unpack_archive without a filter,
-            # but filter doesn't work well for zip files, so we suppress the warning until we find a better solution.
-            # https://github.com/python/cpython/issues/112760
-            warnings.simplefilter("ignore")
-            shutil.unpack_archive(tarballpath, self.build_dir)
+        # Use a Python 3.14-like filter (see https://github.com/python/cpython/issues/112760)
+        # Can be removed once we use Python 3.14
+        # The "data" filter will reset ownership but preserve permissions and modification times
+        # Without it, permissions and modification times will be silently skipped if the uid/git
+        # is too large for the chown() call. This behavior can lead to "Permission denied" errors
+        # (missing x bit) or random strange `make` behavior (due to wrong mtime order) in the CI
+        # pipeline.
+        shutil.unpack_archive(
+            tarballpath,
+            self.build_dir,
+            filter=None if tarballpath.suffix == ".zip" else "data",
+        )
 
         extract_dir_name = self.source_metadata.extract_dir
         if extract_dir_name is None: