diff --git a/src/session_recall/metadocs/cli.py b/src/session_recall/metadocs/cli.py
index d087c5e..da92358 100644
--- a/src/session_recall/metadocs/cli.py
+++ b/src/session_recall/metadocs/cli.py
@@ -89,6 +89,8 @@ def run(args: argparse.Namespace) -> int:
         return 0
 
     if cmd == "run":
+        import os as _os
+        from .run import acquire_lock
         distiller = make_distiller(cfg.engine)
         if distiller is None:
             print(f"unknown engine {cfg.engine!r} in metadocs.json")
@@ -96,11 +98,18 @@ def run(args: argparse.Namespace) -> int:
         if not app_config.DB_PATH.exists():
             print(f"no index at {app_config.DB_PATH} — run: session-recall index")
             return 1
+        lock_fd = acquire_lock(app_config.DATA_DIR)
+        if lock_fd is None:
+            # exit 0 on purpose: the overlap is expected (nightly job vs a long
+            # manual backfill), and the other run is doing this run's work
+            print("another meta docs run is already in progress — stepping aside")
+            return 0
         db = open_index(app_config.DB_PATH)
         try:
             report = run_once(cfg, db, distiller)
         finally:
             db.close()
+            _os.close(lock_fd)
         print(report.summary())
         return 1 if report.blocked else 0
 
diff --git a/src/session_recall/metadocs/run.py b/src/session_recall/metadocs/run.py
index e044ad5..4e0e7dc 100644
--- a/src/session_recall/metadocs/run.py
+++ b/src/session_recall/metadocs/run.py
@@ -10,6 +10,8 @@
 Other projects still run; each project that changed gets its own commit.
 """
 
+import fcntl
+import os
 from dataclasses import dataclass, field
 from pathlib import Path
 
@@ -19,6 +21,22 @@
 from .repo import commit, current_docs, ensure_repo, write_docs
 
 
+def acquire_lock(data_dir: Path) -> int | None:
+    """One run at a time. Runs are hours-long during a backfill, so the
+    nightly launchd job WILL overlap a manual run sooner or later — and two
+    runs would race each other over watermarks and the git repo. flock, not a
+    pid file: the lock dies with the process, so a crash never wedges the job.
+    Returns the fd holding the lock, or None when another run owns it."""
+    data_dir.mkdir(parents=True, exist_ok=True)
+    fd = os.open(data_dir / "metadocs.lock", os.O_CREAT | os.O_WRONLY, 0o600)
+    try:
+        fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB)
+    except OSError:
+        os.close(fd)
+        return None
+    return fd
+
+
 @dataclass
 class RunReport:
     projects: list = field(default_factory=list)   # (project, done, pending, note)
diff --git a/tests/test_metadocs.py b/tests/test_metadocs.py
index 88243e4..17a2a19 100644
--- a/tests/test_metadocs.py
+++ b/tests/test_metadocs.py
@@ -257,6 +257,18 @@ def test_run_commit_per_project(db, tmp_path, repo, monkeypatch):
     assert "meta docs: proj — 1 session(s)" in log
 
 
+# -- single-run lock ----------------------------------------------------------
+def test_second_run_steps_aside_while_first_holds_lock(tmp_path):
+    import os
+    fd = run_mod.acquire_lock(tmp_path)
+    assert fd is not None
+    assert run_mod.acquire_lock(tmp_path) is None    # nightly vs manual overlap
+    os.close(fd)
+    fd2 = run_mod.acquire_lock(tmp_path)             # released with the process
+    assert fd2 is not None
+    os.close(fd2)
+
+
 # -- schedule -----------------------------------------------------------------
 def test_plist_shape(tmp_path):
     plist = schedule.build_plist("21:30", tmp_path / "m.log")