diff --git a/tools/gen-cpydiff.py b/tools/gen-cpydiff.py
index aff5b56e7b..8aef375149 100644
--- a/tools/gen-cpydiff.py
+++ b/tools/gen-cpydiff.py
@@ -39,10 +39,10 @@ from collections import namedtuple
 # to the correct executable.
 if os.name == 'nt':
     CPYTHON3 = os.getenv('MICROPY_CPYTHON3', 'python3.exe')
-    MICROPYTHON = os.getenv('MICROPY_MICROPYTHON', '../windows/micropython.exe')
+    MICROPYTHON = os.getenv('MICROPY_MICROPYTHON', '../ports/windows/micropython.exe')
 else:
     CPYTHON3 = os.getenv('MICROPY_CPYTHON3', 'python3')
-    MICROPYTHON = os.getenv('MICROPY_MICROPYTHON', '../unix/micropython')
+    MICROPYTHON = os.getenv('MICROPY_MICROPYTHON', '../ports/unix/micropython')
 
 TESTPATH = '../tests/cpydiff/'
 DOCPATH = '../docs/genrst/'