diff --git a/src/security_scanner/runtime/incremental_discovery.py b/src/security_scanner/runtime/incremental_discovery.py
index dcc8ed2..340634b 100644
--- a/src/security_scanner/runtime/incremental_discovery.py
+++ b/src/security_scanner/runtime/incremental_discovery.py
@@ -5,9 +5,10 @@
 import datetime as dt
 import fnmatch
 import subprocess
+from collections.abc import Callable, Sequence
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Callable, Protocol, Sequence
+from typing import Protocol
 
 from security_scanner.catalog.scan_target import ScanTarget
 from security_scanner.runtime.poll_fetch import (
@@ -33,7 +34,6 @@
     ScanLedgerKey,
 )
 
-
 DISCOVERY_MODE_INITIALIZE = "initialize"
 DISCOVERY_MODE_ENQUEUE = "enqueue"
 DEFAULT_REF_PATTERNS = ("refs/remotes/origin/*",)
@@ -115,7 +115,15 @@ def list_remote_refs(
         return refs
 
     def is_ancestor(self, repo_path: Path, old_sha: str, new_sha: str) -> bool:
-        cmd = ["git", "-C", str(repo_path), "merge-base", "--is-ancestor", old_sha, new_sha]
+        cmd = [
+            "git",
+            "-C",
+            str(repo_path),
+            "merge-base",
+            "--is-ancestor",
+            old_sha,
+            new_sha,
+        ]
         try:
             subprocess.run(cmd, check=True, capture_output=True, text=True)
             return True
@@ -489,6 +497,15 @@ def run_incremental_discovery(
 
         fetch_ok += 1
         refs_observed += len(refs)
+        if not refs:
+            advance = getattr(request.store, "advance_repo_health", None)
+            if advance is not None:
+                advance(
+                    repo_id,
+                    job_type=JOB_TYPE_INCREMENTAL,
+                    completed_at=_now(request),
+                )
+            continue
 
         for git_ref in refs:
             current_state = request.store.get_ref_state(repo_id, git_ref.ref_name)
diff --git a/tests/test_incremental_discovery.py b/tests/test_incremental_discovery.py
index 3924bad..80a0119 100644
--- a/tests/test_incremental_discovery.py
+++ b/tests/test_incremental_discovery.py
@@ -17,7 +17,6 @@
 from security_scanner.storage.adapters.nosql_db.items import repo_id_for_scan_target_url
 from security_scanner.storage.base import RefState, ScanJob, ScanLedgerKey
 
-
 NOW = dt.datetime(2026, 6, 12, 10, 0, tzinfo=dt.UTC)
 TARGET = ScanTarget(
     url="https://github.com/example-org/example-repo",
@@ -36,6 +35,7 @@ def __init__(self, targets: list[ScanTarget]) -> None:
         self.ref_states: dict[tuple[str, str], RefState] = {}
         self.jobs: dict[str, ScanJob] = {}
         self.ledger: set[ScanLedgerKey] = set()
+        self.health_advances: list[tuple[str, str, dt.datetime]] = []
 
     def list_scan_targets(self) -> list[ScanTarget]:
         return list(self.targets)
@@ -62,6 +62,9 @@ def enqueue_commit_scan_job(self, job: ScanJob) -> bool:
         self.jobs[job.job_id] = job
         return True
 
+    def advance_repo_health(self, repo_id: str, *, job_type: str, completed_at) -> None:
+        self.health_advances.append((repo_id, job_type, completed_at))
+
 
 class FakeGitDiscovery:
     def __init__(self) -> None:
@@ -182,7 +185,9 @@ def test_enqueue_creates_one_job_per_new_unscanned_commit_and_advances_ref_state
 
     assert summary.jobs_enqueued == 2
     assert {job.commit_sha for job in store.jobs.values()} == {MID_SHA, NEW_SHA}
-    assert {job.commit_range for job in store.jobs.values()} == {f"{OLD_SHA}..{NEW_SHA}"}
+    assert {job.commit_range for job in store.jobs.values()} == {
+        f"{OLD_SHA}..{NEW_SHA}"
+    }
     assert store.ref_states[(repo_id, REF_MAIN)].last_seen_sha == NEW_SHA
 
 
@@ -207,6 +212,29 @@ def test_enqueue_missing_ref_state_observes_without_backfill():
     assert store.ref_states[(repo_id, REF_MAIN)].last_seen_sha == NEW_SHA
 
 
+def test_enqueue_no_refs_marks_repo_incrementally_fresh_without_job():
+    repo_path = Path("/synthetic-cache/example-repo")
+    repo_id = repo_id_for_scan_target_url(TARGET.url)
+    store = FakeIncrementalStore([TARGET])
+    git = FakeGitDiscovery()
+    git.refs_by_path[repo_path] = []
+
+    summary = run_incremental_discovery(
+        _request(
+            mode=DISCOVERY_MODE_ENQUEUE,
+            store=store,
+            git=git,
+            fetch_repo=lambda url: repo_path,
+        )
+    )
+
+    assert summary.fetch_ok == 1
+    assert summary.refs_observed == 0
+    assert summary.jobs_enqueued == 0
+    assert store.jobs == {}
+    assert store.health_advances == [(repo_id, "incremental", NOW)]
+
+
 def test_enqueue_skips_commits_present_in_ledger():
     repo_path = Path("/synthetic-cache/example-repo")
     repo_id = repo_id_for_scan_target_url(TARGET.url)