diff --git a/Tools/wasm/emscripten/__main__.py b/Tools/wasm/emscripten/__main__.py
index b855e80cda703c..b25cbb01dedd31 100644
--- a/Tools/wasm/emscripten/__main__.py
+++ b/Tools/wasm/emscripten/__main__.py
@@ -186,7 +186,7 @@ def make_emscripten_libffi(context, working_dir):
 def configure_emscripten_python(context, working_dir):
     """Configure the emscripten/host build."""
     config_site = os.fsdecode(
-        CHECKOUT / "Tools" / "wasm" / "config.site-wasm32-emscripten"
+        EMSCRIPTEN_DIR / "config.site-wasm32-emscripten"
     )
 
     emscripten_build_dir = working_dir.relative_to(CHECKOUT)
diff --git a/Tools/wasm/config.site-wasm32-emscripten b/Tools/wasm/emscripten/config.site-wasm32-emscripten
similarity index 97%
rename from Tools/wasm/config.site-wasm32-emscripten
rename to Tools/wasm/emscripten/config.site-wasm32-emscripten
index 1471546a5eec17..8c3a338dacb2dc 100644
--- a/Tools/wasm/config.site-wasm32-emscripten
+++ b/Tools/wasm/emscripten/config.site-wasm32-emscripten
@@ -1,6 +1,6 @@
 # config.site override for cross compiling to wasm32-emscripten platform
 #
-# CONFIG_SITE=Tools/wasm/config.site-wasm32-emscripten \
+# CONFIG_SITE=Tools/wasm/emscripten/config.site-wasm32-emscripten \
 #     emconfigure ./configure --host=wasm32-unknown-emscripten --build=...
 #
 # Written by Christian Heimes <christian@python.org>