diff --git a/tools/pygrub/Makefile b/tools/pygrub/Makefile
index 75bf46bc83..fab70ffc30 100644
--- a/tools/pygrub/Makefile
+++ b/tools/pygrub/Makefile
@@ -11,7 +11,7 @@ build:
 .PHONY: install
 ifndef XEN_PYTHON_NATIVE_INSTALL
 install: all
-	CFLAGS="$(CFLAGS)" python setup.py install --home="$(DESTDIR)/usr"
+	CFLAGS="$(CFLAGS)" python setup.py install --home="$(DESTDIR)/usr" --prefix=""
 else
 install: all
 	CFLAGS="$(CFLAGS)" python setup.py install --root="$(DESTDIR)"
diff --git a/tools/python/Makefile b/tools/python/Makefile
index b3e404cb9f..e73d624414 100644
--- a/tools/python/Makefile
+++ b/tools/python/Makefile
@@ -11,7 +11,7 @@ build:
 .PHONY: install
 ifndef XEN_PYTHON_NATIVE_INSTALL
 install: all
-	CFLAGS="$(CFLAGS)" python setup.py install --home="$(DESTDIR)/usr" --force
+	CFLAGS="$(CFLAGS)" python setup.py install --home="$(DESTDIR)/usr" --prefix="" --force
 else
 install: all
 	CFLAGS="$(CFLAGS)" python setup.py install --root="$(DESTDIR)" --force