diff --git a/tools/makemanifest.py b/tools/makemanifest.py
index d059d4a2660fe..9dd8815aac5f7 100644
--- a/tools/makemanifest.py
+++ b/tools/makemanifest.py
@@ -29,7 +29,8 @@
 import os
 import subprocess
 
-sys.path.append(os.path.join(os.path.dirname(__file__), "../mpy-cross"))
+# Always use the mpy-cross from this repo.
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../mpy-cross"))
 import mpy_cross
 
 import manifestfile