diff --git a/loopx/contract.py b/loopx/contract.py
index ae1db7a0f8..1549b89712 100644
--- a/loopx/contract.py
+++ b/loopx/contract.py
@@ -750,16 +750,22 @@ def iter_scan_files(scan_root: Path) -> list[Path]:
     files: list[Path] = []
     tracked_files = _tracked_scan_files(scan_root)
     root_parts = set(scan_root.parts)
-    if any(part in DEFAULT_SKIP_DIRS or part.endswith(".egg-info") for part in root_parts):
+    # Dependency pruning never overrides tracked repository ownership.
+    if (
+        any(part in DEFAULT_SKIP_DIRS or part.endswith(".egg-info") for part in root_parts)
+        or os.path.isfile(scan_root / "pyvenv.cfg")
+    ):
         return sorted(tracked_files)
 
     for dir_path, dir_names, file_names in os.walk(scan_root):
+        current_dir = Path(dir_path)
         dir_names[:] = [
             name
             for name in dir_names
-            if name not in DEFAULT_SKIP_DIRS and not name.endswith(".egg-info")
+            if name not in DEFAULT_SKIP_DIRS
+            and not name.endswith(".egg-info")
+            and not os.path.isfile(current_dir / name / "pyvenv.cfg")
         ]
-        current_dir = Path(dir_path)
         for file_name in file_names:
             path = (current_dir / file_name).resolve()
             if path.name.endswith(".local.json"):
diff --git a/tests/test_contract_scan_unreadable_files.py b/tests/test_contract_scan_unreadable_files.py
index 9968fb9b7b..e508ea336e 100644
--- a/tests/test_contract_scan_unreadable_files.py
+++ b/tests/test_contract_scan_unreadable_files.py
@@ -80,3 +80,32 @@ def test_scan_public_boundary_reports_unreadable_file(tmp_path: Path) -> None:
 
     assert payload["ok"] is True
     assert payload["unreadable_files"] == ["locked.md: Permission denied"]
+
+
+def test_virtualenv_pruning_preserves_tracked_and_explicit_scan_targets(tmp_path: Path) -> None:
+    repo = tmp_path / "repo"
+    env = repo / "custom-python"
+    env.mkdir(parents=True)
+    (env / "pyvenv.cfg").write_text("include-system-site-packages = false\n")
+    payload = 'AUTH = "' + "tok" + 'en=syntheticsyntheticsynthetic"\n'
+    dependency = env / "dependency.py"
+    owned = env / "owned.py"
+    unmarked = repo / "unmarked" / "dependency.py"
+    unmarked.parent.mkdir()
+    for path in (dependency, owned, unmarked):
+        path.write_text(payload)
+    subprocess.run(["git", "init", "-q", str(repo)], check=True, capture_output=True)
+    subprocess.run(["git", "-C", str(repo), "add", "custom-python/owned.py"], check=True)
+
+    # Marked dependencies are omitted; owned content cannot hide behind a marker.
+    assert iter_scan_files(repo) == sorted([owned, unmarked])
+    assert iter_scan_files(env) == [owned]
+    result = scan_public_boundary([repo])
+    assert result["scanned_files"] == 2
+    assert result["ok"] is False
+    assert any("custom-python/owned.py" in hit for hit in result["hits"])
+    # An explicit file remains an explicit request even inside a pruned tree.
+    assert iter_scan_files(dependency) == [dependency]
+    assert scan_public_boundary([dependency])["hits"]
+    (env / "pyvenv.cfg").unlink()
+    assert dependency in iter_scan_files(repo)