diff --git a/headroom/cli/wrap.py b/headroom/cli/wrap.py
index 06de0cc87..8c0f33b2a 100644
--- a/headroom/cli/wrap.py
+++ b/headroom/cli/wrap.py
@@ -1840,6 +1840,27 @@ def _scope_serena_languages(*, verbose: bool = False) -> None:
             click.echo(f"  Serena: could not scope languages ({e})")
 
 
+def _serena_project_skip_reason(root: Path) -> str | None:
+    """Why Serena's per-project setup must not run for *root* (None = proceed).
+
+    ``$HOME`` is never a project: scanning it walks every unrelated tree
+    (Downloads, VM images, network mounts) and would write ``project.yml`` into
+    Serena's own ``~/.serena`` config directory. A linked git worktree (its
+    top-level ``.git`` is a file, not a directory) is an ephemeral checkout that
+    would pay for its own index at a path that soon disappears.
+    """
+    try:
+        resolved = root.resolve()
+        home = Path.home().resolve()
+    except OSError:
+        return None
+    if resolved == home:
+        return "$HOME is not a project"
+    if (resolved / ".git").is_file():
+        return "linked git worktree"
+    return None
+
+
 def _index_serena_project(*, verbose: bool = False) -> None:
     """Warm Serena's symbol cache for the current project (non-fatal).
 
@@ -1947,6 +1968,11 @@ def _setup_serena_mcp(
     # ``serena project index`` respects the scope. Each step is best-effort and
     # non-fatal — none of them block the wrap.
     _inject_serena_instructions(_serena_instruction_file(registrar), verbose=verbose)
+    skip_reason = _serena_project_skip_reason(Path.cwd())
+    if skip_reason is not None:
+        if verbose:
+            click.echo(f"  Serena: skipping language scope + pre-index ({skip_reason})")
+        return
     _scope_serena_languages(verbose=verbose)
     _index_serena_project(verbose=verbose)
 
diff --git a/tests/test_cli/test_wrap_serena_boost.py b/tests/test_cli/test_wrap_serena_boost.py
index 49dc7fe09..c5ca1d9c7 100644
--- a/tests/test_cli/test_wrap_serena_boost.py
+++ b/tests/test_cli/test_wrap_serena_boost.py
@@ -258,3 +258,34 @@ def test_preindex_generic_error_is_non_fatal(monkeypatch: pytest.MonkeyPatch) ->
     monkeypatch.setattr(wrap_cli, "run", Mock(side_effect=RuntimeError("boom")))
     # Must not propagate.
     wrap_cli._index_serena_project(verbose=True)
+
+
+# ---------------------------------------------------------------------------
+# _serena_project_skip_reason — keep per-project setup off non-project roots
+# ---------------------------------------------------------------------------
+
+
+def test_skip_reason_none_for_ordinary_project(tmp_path: Path) -> None:
+    assert wrap_cli._serena_project_skip_reason(tmp_path) is None
+
+
+def test_skip_reason_none_for_normal_checkout(tmp_path: Path) -> None:
+    (tmp_path / ".git").mkdir()  # real checkout: .git is a directory
+
+    assert wrap_cli._serena_project_skip_reason(tmp_path) is None
+
+
+def test_skip_reason_flags_home(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    monkeypatch.setattr(Path, "home", classmethod(lambda cls: tmp_path))
+
+    assert wrap_cli._serena_project_skip_reason(tmp_path) == "$HOME is not a project"
+
+
+def test_skip_reason_flags_linked_worktree(tmp_path: Path) -> None:
+    (tmp_path / ".git").write_text("gitdir: /repo/.git/worktrees/wt\n")
+
+    assert wrap_cli._serena_project_skip_reason(tmp_path) == "linked git worktree"
+
+
+def test_skip_reason_survives_unresolvable_root(tmp_path: Path) -> None:
+    assert wrap_cli._serena_project_skip_reason(tmp_path / "gone") is None