diff --git a/backend/app/api/v1/endpoint_modules/ogm_webhook.py b/backend/app/api/v1/endpoint_modules/ogm_webhook.py
index 4ca36d6..95bfc2f 100644
--- a/backend/app/api/v1/endpoint_modules/ogm_webhook.py
+++ b/backend/app/api/v1/endpoint_modules/ogm_webhook.py
@@ -17,7 +17,14 @@
 router = APIRouter()
 
 EVENT_DRIVEN_WATCH_MODES = {"webhook", "both", "nightly"}
-REPOSITORY_DISCOVERY_ACTIONS = {"created", "publicized", "renamed", "transferred", "unarchived"}
+REPOSITORY_DISCOVERY_ACTIONS = {
+    "created",
+    "publicized",
+    "renamed",
+    "transferred",
+    "archived",
+    "unarchived",
+}
 
 
 def _verify_github_signature(body: bytes, signature_header: Optional[str], secret: str) -> bool:
diff --git a/backend/app/services/ogm_harvest/harvest.py b/backend/app/services/ogm_harvest/harvest.py
index a61f455..16564e0 100644
--- a/backend/app/services/ogm_harvest/harvest.py
+++ b/backend/app/services/ogm_harvest/harvest.py
@@ -27,10 +27,17 @@ async def harvest_repo(
     Returns a dict with run_id, repo, commit, stats, and missing_count.
     """
     repo = OGMHarvestRepository()
+    await repo.ensure_repo(repo_name)
+    configured = await repo.get_repo(repo_name)
+    if configured and (
+        not configured.get("ogm_enabled", True)
+        or (configured.get("ogm_tags") or {}).get("ogm_archived", False)
+    ):
+        return {"ogm_repo_name": repo_name, "status": "skipped", "reason": "disabled or archived"}
+
     syncer = OGMRepoSync(base_dir=checkout_base_dir)
     importer = OGMResourceImporter(repo=repo)
 
-    await repo.upsert_repo(ogm_repo_name=repo_name)
     await repo.mark_repo_harvest_started(repo_name)
     run_id = await repo.create_harvest_run(ogm_repo_name=repo_name, ogm_trigger=trigger)
     run_started_at = datetime.utcnow()
diff --git a/backend/app/services/ogm_harvest/repository.py b/backend/app/services/ogm_harvest/repository.py
index 31ff877..169d12e 100644
--- a/backend/app/services/ogm_harvest/repository.py
+++ b/backend/app/services/ogm_harvest/repository.py
@@ -193,6 +193,13 @@ async def get_repo(self, ogm_repo_name: str) -> Optional[Dict[str, Any]]:
         )
         return dict(row) if row else None
 
+    async def ensure_repo(self, ogm_repo_name: str) -> None:
+        """Create an unknown repo without overwriting existing discovery/admin settings."""
+        stmt = pg_insert(ogm_repos).values(ogm_repo_name=ogm_repo_name)
+        await database.execute(
+            stmt.on_conflict_do_nothing(index_elements=[ogm_repos.c.ogm_repo_name])
+        )
+
     async def upsert_repo(
         self,
         ogm_repo_name: str,
diff --git a/backend/app/tasks/ogm_harvest.py b/backend/app/tasks/ogm_harvest.py
index 4f5ed33..37b788a 100644
--- a/backend/app/tasks/ogm_harvest.py
+++ b/backend/app/tasks/ogm_harvest.py
@@ -71,7 +71,7 @@ async def _ogm_harvest_all_async(trigger: str) -> Dict[str, Any]:
     repos = await repo.list_repos()
     selected = []
     for r in repos:
-        if not r.get("ogm_enabled", True):
+        if not r.get("ogm_enabled", True) or (r.get("ogm_tags") or {}).get("ogm_archived"):
             continue
         mode = (r.get("ogm_watch_mode") or "").lower()
         if trigger.lower() in SCHEDULED_OGM_TRIGGERS and mode not in SCHEDULED_OGM_WATCH_MODES:
diff --git a/backend/scripts/ogm_harvester.py b/backend/scripts/ogm_harvester.py
index dbfa10a..52e4691 100644
--- a/backend/scripts/ogm_harvester.py
+++ b/backend/scripts/ogm_harvester.py
@@ -82,7 +82,11 @@ def docs_to_index(self) -> Generator[Tuple[Dict, str], None, None]:
             self.logger.warning(f"OGM path does not exist: {self.ogm_path}")
             return
 
+        # Old checkouts remain on disk after GitHub repositories are archived.
+        active_repos = set(self.repositories())
         for json_file in ogm_path.rglob("*.json"):
+            if json_file.relative_to(ogm_path).parts[0] not in active_repos:
+                continue
             # Skip layers.json files
             if json_file.name == "layers.json":
                 self.logger.debug(f"skipping {json_file}; not a geoblacklight JSON document")
diff --git a/backend/scripts/populate_ogm_repos.py b/backend/scripts/populate_ogm_repos.py
index 135d42d..3a3ca3d 100644
--- a/backend/scripts/populate_ogm_repos.py
+++ b/backend/scripts/populate_ogm_repos.py
@@ -217,7 +217,7 @@ def main():
     parser.add_argument(
         "--include-archived",
         action="store_true",
-        help="Include archived repos (default: skip archived)",
+        help="Deprecated compatibility flag; archived repos are always recorded as disabled",
     )
     args = parser.parse_args()
 
@@ -229,8 +229,7 @@ def main():
     sync_db_url = _sync_database_url(database_url)
 
     repos = list_org_repos(args.org, token, per_page=args.per_page)
-    if not args.include_archived:
-        repos = [r for r in repos if not r.get("archived", False)]
+    # Reconcile archived repos too, so previously enabled entries become disabled.
 
     if args.limit:
         repos = repos[: args.limit]
diff --git a/backend/scripts/trigger_ogm_nightly_sync.py b/backend/scripts/trigger_ogm_nightly_sync.py
index 9ba2a35..ac45a38 100755
--- a/backend/scripts/trigger_ogm_nightly_sync.py
+++ b/backend/scripts/trigger_ogm_nightly_sync.py
@@ -52,7 +52,7 @@ def main() -> None:
     parser.add_argument(
         "--include-archived",
         action="store_true",
-        help="Include archived repos when refreshing ogm_repos",
+        help="Deprecated compatibility flag; archived repos are always recorded as disabled",
     )
     parser.add_argument(
         "--skip-harvest",
@@ -69,8 +69,7 @@ def main() -> None:
 
     sync_db_url = _sync_database_url(database_url)
     repos = list_org_repos(args.org, token, per_page=args.per_page)
-    if not args.include_archived:
-        repos = [repo for repo in repos if not repo.get("archived", False)]
+    # Reconcile archived repos too, so previously enabled entries become disabled.
     if args.limit is not None:
         repos = repos[: args.limit]
 
diff --git a/backend/tests/api/v1/test_ogm_webhook.py b/backend/tests/api/v1/test_ogm_webhook.py
index f4cc792..05d4f19 100644
--- a/backend/tests/api/v1/test_ogm_webhook.py
+++ b/backend/tests/api/v1/test_ogm_webhook.py
@@ -218,3 +218,19 @@ def test_push_to_unknown_aardvark_repo_discovers_and_queues(monkeypatch):
     assert response.json()["queued"] == "edu.new"
     assert queued == [{"repo_name": "edu.new", "trigger": "push"}]
     assert FakeRepo.upserts[0]["ogm_repo_name"] == "edu.new"
+
+
+def test_repository_archived_disables_existing_repo_without_queuing(monkeypatch):
+    queued = []
+    FakeRepo.rows = {"edu.umn": {"ogm_enabled": True, "ogm_watch_mode": "both"}}
+    monkeypatch.setenv("OGM_WEBHOOK_SECRET", SECRET)
+    monkeypatch.setattr(ogm_webhook, "OGMHarvestRepository", FakeRepo)
+    monkeypatch.setattr(ogm_webhook, "repo_has_metadata_aardvark", lambda *args: True)
+    monkeypatch.setattr(ogm_webhook.ogm_harvest_repo, "delay", lambda **kw: queued.append(kw))
+    response = _post_webhook(
+        {"action": "archived", "repository": _repo_payload("edu.umn", archived=True)}, "repository"
+    )
+    assert response.status_code == 200
+    assert FakeRepo.rows["edu.umn"]["ogm_enabled"] is False
+    assert FakeRepo.rows["edu.umn"]["ogm_tags"]["ogm_archived"] is True
+    assert queued == []
diff --git a/backend/tests/scripts/test_ogm_harvester.py b/backend/tests/scripts/test_ogm_harvester.py
new file mode 100644
index 0000000..b513117
--- /dev/null
+++ b/backend/tests/scripts/test_ogm_harvester.py
@@ -0,0 +1,23 @@
+import json
+
+from scripts.ogm_harvester import OGMHarvester
+
+
+def test_docs_to_index_excludes_archived_checkouts(tmp_path, monkeypatch):
+    for repo in ("edu.umn", "geobtaa"):
+        directory = tmp_path / repo / "metadata-aardvark"
+        directory.mkdir(parents=True)
+        (directory / "record.json").write_text(
+            json.dumps(
+                {
+                    "id": "same-migrated-record",
+                    "gbl_mdVersion_s": "Aardvark",
+                    "source": repo,
+                }
+            )
+        )
+    harvester = OGMHarvester(ogm_path=str(tmp_path))
+    monkeypatch.setattr(harvester, "repositories", lambda: ["geobtaa"])
+    records = list(harvester.docs_to_index())
+    assert len(records) == 1
+    assert records[0][0]["source"] == "geobtaa"
diff --git a/backend/tests/scripts/test_populate_ogm_repos.py b/backend/tests/scripts/test_populate_ogm_repos.py
index 4187777..dce38e8 100644
--- a/backend/tests/scripts/test_populate_ogm_repos.py
+++ b/backend/tests/scripts/test_populate_ogm_repos.py
@@ -1,5 +1,7 @@
 import json
 
+import pytest
+
 from scripts import populate_ogm_repos
 
 
@@ -62,3 +64,39 @@ def fake_get(url, headers, params, timeout):
     )
     assert calls[0]["headers"]["Authorization"] == "Bearer bad-token"
     assert "Authorization" not in calls[1]["headers"]
+
+
+@pytest.mark.parametrize("script_name", ["populate_ogm_repos", "trigger_ogm_nightly_sync"])
+@pytest.mark.parametrize("extra_args", [[], ["--include-archived"]])
+def test_refresh_disables_archived_repos_and_enables_geobtaa(monkeypatch, script_name, extra_args):
+    from importlib import import_module
+
+    script = import_module(f"scripts.{script_name}")
+    monkeypatch.setenv("DATABASE_URL", "postgresql://unused/test")
+    args = [script_name, *extra_args]
+    if script_name == "trigger_ogm_nightly_sync":
+        args.append("--skip-harvest")
+    monkeypatch.setattr("sys.argv", args)
+    monkeypatch.setattr(
+        script,
+        "list_org_repos",
+        lambda *a, **kw: [
+            {"name": "edu.umn", "archived": True},
+            {"name": "geobtaa", "archived": False},
+        ],
+    )
+    monkeypatch.setattr(script, "repo_has_metadata_aardvark", lambda *a: True)
+    rows = []
+
+    def capture(url, values, dry_run=False):
+        rows.extend(values)
+        return len(values), 0
+
+    monkeypatch.setattr(script, "upsert_rows", capture)
+    script.main()
+    assert [(r["ogm_repo_name"], r["ogm_enabled"]) for r in rows] == [
+        ("edu.umn", False),
+        ("geobtaa", True),
+    ]
+    assert rows[0]["ogm_watch_mode"] == "manual"
+    assert rows[0]["ogm_tags"]["ogm_archived"] is True
diff --git a/backend/tests/services/test_ogm_search_index.py b/backend/tests/services/test_ogm_search_index.py
index 10504a5..d705196 100644
--- a/backend/tests/services/test_ogm_search_index.py
+++ b/backend/tests/services/test_ogm_search_index.py
@@ -37,7 +37,7 @@ async def test_harvest_requires_search_sync_before_reporting_success(monkeypatch
 
     repo = MagicMock()
     for name in (
-        "upsert_repo",
+        "ensure_repo",
         "mark_repo_harvest_started",
         "cancel_other_running_runs",
         "update_harvest_run",
@@ -45,6 +45,7 @@ async def test_harvest_requires_search_sync_before_reporting_success(monkeypatch
         "mark_repo_harvest_completed",
     ):
         setattr(repo, name, AsyncMock())
+    repo.get_repo = AsyncMock(return_value={"ogm_enabled": True})
     repo.create_harvest_run = AsyncMock(return_value=1)
     importer = MagicMock(changed_thumbnail_resource_ids=set())
     importer.upsert_stream = AsyncMock(return_value={"imported": 1, "errors": 0})
@@ -72,3 +73,40 @@ async def test_harvest_requires_search_sync_before_reporting_success(monkeypatch
         assert result["stats"]["search_index"] == {"indexed": 1, "errors": 0}
         assert repo.finalize_harvest_run.await_args.kwargs["ogm_status"] == "success"
     search.assert_awaited_once_with("repo")
+
+
+@pytest.mark.asyncio
+@pytest.mark.parametrize(
+    "settings",
+    [
+        {"ogm_enabled": False},
+        {"ogm_enabled": True, "ogm_tags": {"ogm_archived": True}},
+    ],
+)
+async def test_harvest_skips_disabled_or_archived_repo(monkeypatch, settings):
+    from app.services.ogm_harvest import harvest
+
+    repo = MagicMock()
+    repo.ensure_repo = AsyncMock()
+    repo.get_repo = AsyncMock(return_value=settings)
+    syncer = MagicMock()
+    monkeypatch.setattr(harvest, "OGMHarvestRepository", lambda: repo)
+    monkeypatch.setattr(harvest, "OGMRepoSync", syncer)
+    result = await harvest.harvest_repo("edu.umn", trigger="push")
+    assert result["status"] == "skipped"
+    syncer.assert_not_called()
+    repo.upsert_repo.assert_not_called()
+    repo.mark_repo_harvest_started.assert_not_called()
+
+
+@pytest.mark.asyncio
+async def test_ensure_repo_does_not_overwrite_catalog_settings(monkeypatch):
+    from sqlalchemy.dialects import postgresql
+
+    from app.services.ogm_harvest import repository
+
+    execute = AsyncMock()
+    monkeypatch.setattr(repository.database, "execute", execute)
+    await repository.OGMHarvestRepository().ensure_repo("geobtaa")
+    statement = str(execute.await_args.args[0].compile(dialect=postgresql.dialect()))
+    assert "ON CONFLICT (ogm_repo_name) DO NOTHING" in statement
diff --git a/backend/tests/tasks/test_ogm_harvest_tasks.py b/backend/tests/tasks/test_ogm_harvest_tasks.py
index 6f9ac54..cf3fe65 100644
--- a/backend/tests/tasks/test_ogm_harvest_tasks.py
+++ b/backend/tests/tasks/test_ogm_harvest_tasks.py
@@ -19,6 +19,12 @@ async def test_ogm_harvest_all_nightly_trigger_selects_scheduled_modes(monkeypat
             {"ogm_repo_name": "scheduled-repo", "ogm_enabled": True, "ogm_watch_mode": "scheduled"},
             {"ogm_repo_name": "both-repo", "ogm_enabled": True, "ogm_watch_mode": "both"},
             {"ogm_repo_name": "manual-repo", "ogm_enabled": True, "ogm_watch_mode": "manual"},
+            {
+                "ogm_repo_name": "archived-repo",
+                "ogm_enabled": True,
+                "ogm_watch_mode": "both",
+                "ogm_tags": {"ogm_archived": True},
+            },
             {"ogm_repo_name": "disabled-repo", "ogm_enabled": False, "ogm_watch_mode": "nightly"},
         ]
     )
diff --git a/docs/harvester.md b/docs/harvester.md
index 92f0f86..980d7e0 100644
--- a/docs/harvester.md
+++ b/docs/harvester.md
@@ -80,3 +80,13 @@ representations that may contain an older asset URL. This refresh can be disable
 with `OGM_THUMBNAIL_REFRESH_ENABLED=false`; a refresh failure is recorded in the
 harvest statistics and does not turn an otherwise successful metadata harvest
 into a failure.
+
+Repository discovery always reconciles archived GitHub repositories into the
+catalog as disabled with manual watch mode, including repositories that were
+previously enabled. The legacy `--include-archived` flag is accepted for
+compatibility but is no longer needed. Archived BTAA repositories are replaced
+by the active `geobtaa` repository. Harvest jobs check the saved enabled/archive
+status before pulling and preserve catalog settings when starting a run.
+The standalone harvester also excludes archived checkouts when streaming records.
+Existing records are retained until refreshed from their current source; disabling
+a repository does not delete its previously harvested records.