diff --git a/colcon_core/task/python/build.py b/colcon_core/task/python/build.py
index a72c1a54..5320a939 100644
--- a/colcon_core/task/python/build.py
+++ b/colcon_core/task/python/build.py
@@ -70,6 +70,7 @@ async def build(self, *, additional_hooks=None):  # noqa: D102
             Path(__file__).parent / 'template' / 'sitecustomize.py.em',
             prefix_override / 'sitecustomize.py',
             {
+                'current_prefix': sys.prefix,
                 'site_prefix': args.install_base,
             })
 
diff --git a/colcon_core/task/python/template/sitecustomize.py.em b/colcon_core/task/python/template/sitecustomize.py.em
index bbcd662c..b6bbe2f0 100644
--- a/colcon_core/task/python/template/sitecustomize.py.em
+++ b/colcon_core/task/python/template/sitecustomize.py.em
@@ -1,4 +1,4 @@
 import sys
-if sys.prefix == sys.base_prefix:
+if sys.prefix == @repr(current_prefix):
     sys.real_prefix = sys.prefix
     sys.prefix = sys.exec_prefix = @repr(site_prefix)