diff --git a/pkgs/development/interpreters/python/sitecustomize.py b/pkgs/development/interpreters/python/sitecustomize.py
index e59d6070cb6..72ce951328f 100644
--- a/pkgs/development/interpreters/python/sitecustomize.py
+++ b/pkgs/development/interpreters/python/sitecustomize.py
@@ -21,10 +21,19 @@ paths = os.environ.pop('NIX_PYTHONPATH', None)
 if paths:
     functools.reduce(lambda k, p: site.addsitedir(p, k), paths.split(':'), site._init_pathinfo())
 
-prefixes = os.environ.pop('NIX_PYTHONPREFIX', None)
-if prefixes:
-    site.PREFIXES.extend(prefixes.split(':'))
+# Check whether we are in a venv. 
+# Note Python 2 does not support base_prefix so we assume we are not in a venv.
+in_venv = sys.version_info.major == 3 and sys.prefix != sys.base_prefix
 
-executable = os.environ.pop('NIX_PYTHONEXECUTABLE', None)
-if 'PYTHONEXECUTABLE' not in os.environ and executable:
-    sys.executable = executable
+if not in_venv:
+    executable = os.environ.pop('NIX_PYTHONEXECUTABLE', None)
+    prefix = os.environ.pop('NIX_PYTHONPREFIX', None)
+
+    if 'PYTHONEXECUTABLE' not in os.environ and executable is not None:
+        sys.executable = executable
+    if prefix is not None:
+        # Because we cannot check with Python 2 whether we are in a venv, 
+        # creating a venv from a Nix env won't work as well with Python 2.
+        # Also, note that sysconfig does not like it when sys.prefix is set to None
+        sys.prefix = sys.exec_prefix = prefix
+        site.PREFIXES.insert(0, prefix)
diff --git a/pkgs/development/interpreters/python/tests/test_python.py b/pkgs/development/interpreters/python/tests/test_python.py
index 93aa2bb2b9e..011978c6254 100644
--- a/pkgs/development/interpreters/python/tests/test_python.py
+++ b/pkgs/development/interpreters/python/tests/test_python.py
@@ -27,7 +27,7 @@ class TestCasePython(unittest.TestCase):
     def test_interpreter(self):
         self.assertEqual(sys.executable, INTERPRETER)
 
-    @unittest.skipIf(IS_NIXENV or IS_PYPY, "Prefix is incorrect and needs to be fixed.")
+    @unittest.skipIf(IS_PYPY, "Prefix is incorrect and needs to be fixed.")
     def test_prefix(self):
         self.assertEqual(sys.prefix, ENV)
         self.assertEqual(sys.prefix, sys.exec_prefix)
@@ -37,7 +37,7 @@ class TestCasePython(unittest.TestCase):
 
     @unittest.skipIf(IS_PYPY or sys.version_info.major==2, "Python 2 does not have base_prefix")
     def test_base_prefix(self):
-        if IS_VENV:
+        if IS_VENV or IS_NIXENV:
             self.assertNotEqual(sys.prefix, sys.base_prefix)
         else:
             self.assertEqual(sys.prefix, sys.base_prefix)