diff --git a/cpython/Makefile b/cpython/Makefile
index dc1a4e3b3..b6c0e613b 100644
--- a/cpython/Makefile
+++ b/cpython/Makefile
@@ -25,7 +25,8 @@ $(INSTALL)/lib/$(LIB): $(BUILD)/$(LIB)
 		touch $(BUILD)/$(LIB) ; \
 		emmake make HOSTPYTHON=$(HOSTPYTHON) PYTHON_FOR_BUILD=$(HOSTPYTHON) CROSS_COMPILE=yes inclinstall libinstall $(LIB) && \
 		cp $(LIB) $(INSTALL)/lib/ && \
-		cp $(HOSTINSTALL)/lib/python$(PYMINOR)/`$(HOSTPYTHON) -c "import sysconfig; print(sysconfig._get_sysconfigdata_name())"`.py $(INSTALL)/lib/python$(PYMINOR)/_sysconfigdata__emscripten_.py \
+		cp $(HOSTINSTALL)/lib/python$(PYMINOR)/`$(HOSTPYTHON) -c "import sysconfig; print(sysconfig._get_sysconfigdata_name())"`.py $(INSTALL)/lib/python$(PYMINOR)/_sysconfigdata__emscripten_.py; \
+		sed -i -e 's#'"$(PYODIDE_ROOT)"'##g' $(INSTALL)/lib/python$(PYMINOR)/_sysconfigdata__emscripten_.py; \
 	)