diff --git a/constructor/nsis/main.nsi.tmpl b/constructor/nsis/main.nsi.tmpl
index da08f58bf..1bb81ba52 100644
--- a/constructor/nsis/main.nsi.tmpl
+++ b/constructor/nsis/main.nsi.tmpl
@@ -1638,8 +1638,8 @@ Section "Install"
     SetOutPath "{{ env.conda_meta }}"
     File "{{ env.history_abspath }}"
 
-    # Add frozen marker file if configured
 {%- if env.frozen_abspath %}
+    # Add frozen marker file if configured
     SetOutPath "{{ env.conda_meta }}"
     File "{{ env.frozen_abspath }}"
 {%- endif %}
diff --git a/examples/protected_base/construct.yaml b/examples/protected_base/construct.yaml
index c43044761..7e2e09a49 100644
--- a/examples/protected_base/construct.yaml
+++ b/examples/protected_base/construct.yaml
@@ -12,13 +12,18 @@ specs:
   - python
   - conda
 
+freeze_base:
+  conda: {}
+
 extra_envs:
-  default:
+  env1:
     specs:
       - python
       - pip
       - conda
+    freeze_env:
+      conda:
+        message: This environment is frozen.
 
 extra_files:
-  - frozen.json: conda-meta/frozen
-  - frozen.json: envs/default/conda-meta/frozen
+  - frozen.json: envs/env2/conda-meta/frozen
diff --git a/examples/protected_base/frozen.json b/examples/protected_base/frozen.json
index 0967ef424..087c29648 100644
--- a/examples/protected_base/frozen.json
+++ b/examples/protected_base/frozen.json
@@ -1 +1 @@
-{}
+{"message": "This env is frozen via extra_files."}
diff --git a/tests/test_examples.py b/tests/test_examples.py
index e68d04052..49f3c6149 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -20,6 +20,7 @@
 from conda.core.prefix_data import PrefixData
 from conda.models.version import VersionOrder as Version
 from ruamel.yaml import YAML
+from contextlib import nullcontext
 
 from constructor.utils import (
     StandaloneExe,
@@ -1509,32 +1510,44 @@ def test_not_in_installed_menu_list_(tmp_path, request, no_registry):
         CONDA_EXE == StandaloneExe.CONDA
         and check_version(CONDA_EXE_VERSION, min_version="25.5.0", max_version="25.7.0")
     ),
-    reason="conda-standalone 25.5.x fails with protected environments and older versions ignore frozen files",
+    reason="conda-standalone 25.5.x fails with protected environments",
     strict=True,
 )
-def test_frozen_environment(tmp_path, request):
-    input_path = _example_path("protected_base")
-    for installer, install_dir in create_installer(input_path, tmp_path):
-        _run_installer(
-            input_path,
-            installer,
-            install_dir,
-            request=request,
-            uninstall=False,
-        )
+@pytest.mark.parametrize(
+    "has_conflict",
+    (
+        pytest.param(True, id="with-conflict"),
+        pytest.param(False, id="without-conflict"),
+    ),
+)
+def test_frozen_environment(tmp_path, request, has_conflict):
+    example_path = _example_path("protected_base")
+    input_path = tmp_path / "input"
 
-        expected_frozen_paths = {
-            install_dir / "conda-meta" / "frozen",
-            install_dir / "envs" / "default" / "conda-meta" / "frozen",
-        }
+    context = pytest.raises(subprocess.CalledProcessError) if has_conflict else nullcontext()
 
-        actual_frozen_paths = set()
-        for env in install_dir.glob("**/conda-meta/history"):
-            frozen_file = env.parent / "frozen"
-            assert frozen_file.exists()
-            actual_frozen_paths.add(frozen_file)
+    shutil.copytree(str(example_path), str(input_path))
 
-        assert expected_frozen_paths == actual_frozen_paths, (
-            f"Expected: {sorted(str(p) for p in expected_frozen_paths)}\n"
-            f"Found: {sorted(str(p) for p in actual_frozen_paths)}"
-        )
+    with open(input_path / "construct.yaml") as f:
+        config = YAML().load(f)
+
+    if has_conflict:
+        config.setdefault("extra_files", []).append({"frozen.json": "conda-meta/frozen"})
+        with open(input_path / "construct.yaml", "w") as f:
+            YAML().dump(config, f)
+
+    with context as c:
+        for installer, install_dir in create_installer(input_path, tmp_path):
+            _run_installer(input_path, installer, install_dir, request=request, uninstall=False)
+
+            expected_frozen = {
+                install_dir / "conda-meta" / "frozen": config["freeze_base"]["conda"],
+                install_dir / "envs" / "env1" / "conda-meta" / "frozen": config["extra_envs"]["env1"]["freeze_env"]["conda"],
+            }
+
+            for frozen_path, expected_content in expected_frozen.items():
+                assert frozen_path.exists()
+                assert json.loads(frozen_path.read_text()) == expected_content
+
+    if has_conflict:
+        assert all(s in c.value.stderr for s in ("RuntimeError", "freeze_base / freeze_env", "extra_files", "base"))