diff --git a/colcon_core/task/python/template/sitecustomize.py.em b/colcon_core/task/python/template/sitecustomize.py.em
index 5ed6f35ef..bbcd662c8 100644
--- a/colcon_core/task/python/template/sitecustomize.py.em
+++ b/colcon_core/task/python/template/sitecustomize.py.em
@@ -1,3 +1,4 @@
 import sys
-sys.real_prefix = sys.prefix
-sys.prefix = sys.exec_prefix = @repr(site_prefix)
+if sys.prefix == sys.base_prefix:
+    sys.real_prefix = sys.prefix
+    sys.prefix = sys.exec_prefix = @repr(site_prefix)