diff --git a/backend/.sqlx/query-45997fcb4d9d62c7f7011966bf59bdb86e12ce1d0c8e925e738d2645121a5c1f.json b/backend/.sqlx/query-fbe3a876efd1253d2ef086b03366b2bd117ceb6bc152d2abcd45850ff6aecff9.json
similarity index 65%
rename from backend/.sqlx/query-45997fcb4d9d62c7f7011966bf59bdb86e12ce1d0c8e925e738d2645121a5c1f.json
rename to backend/.sqlx/query-fbe3a876efd1253d2ef086b03366b2bd117ceb6bc152d2abcd45850ff6aecff9.json
index f63afbc986..62ec17f0f8 100644
--- a/backend/.sqlx/query-45997fcb4d9d62c7f7011966bf59bdb86e12ce1d0c8e925e738d2645121a5c1f.json
+++ b/backend/.sqlx/query-fbe3a876efd1253d2ef086b03366b2bd117ceb6bc152d2abcd45850ff6aecff9.json
@@ -1,6 +1,6 @@
 {
   "db_name": "PostgreSQL",
-  "query": "DELETE FROM v2_job_completed\n         WHERE id IN (\n             SELECT jc.id FROM v2_job_completed jc\n             LEFT JOIN v2_job j ON j.id = jc.id\n             WHERE jc.completed_at <= now() - ($1::bigint::text || ' s')::interval\n               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) != ALL($3)\n             ORDER BY jc.completed_at ASC\n             LIMIT $2\n             FOR UPDATE OF jc SKIP LOCKED\n         )\n         RETURNING id",
+  "query": "DELETE FROM v2_job_completed\n         WHERE id IN (\n             SELECT jc.id FROM v2_job_completed jc\n             LEFT JOIN v2_job j ON j.id = jc.id\n             WHERE jc.completed_at <= now() - ($1::bigint::text || ' s')::interval\n               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) NOT IN (\n                   SELECT u FROM unnest($3::uuid[]) AS u WHERE u IS NOT NULL\n               )\n             ORDER BY jc.completed_at ASC\n             LIMIT $2\n             FOR UPDATE OF jc SKIP LOCKED\n         )\n         RETURNING id",
   "describe": {
     "columns": [
       {
@@ -20,5 +20,5 @@
       false
     ]
   },
-  "hash": "45997fcb4d9d62c7f7011966bf59bdb86e12ce1d0c8e925e738d2645121a5c1f"
+  "hash": "fbe3a876efd1253d2ef086b03366b2bd117ceb6bc152d2abcd45850ff6aecff9"
 }
diff --git a/backend/src/monitor.rs b/backend/src/monitor.rs
index 68b9d5c867..9827040358 100644
--- a/backend/src/monitor.rs
+++ b/backend/src/monitor.rs
@@ -1532,14 +1532,22 @@ async fn delete_expired_jobs_batch(
     .await?;
 
     // Use FOR UPDATE SKIP LOCKED to avoid contention between replicas
-    // ORDER BY completed_at ensures we delete oldest jobs first
+    // ORDER BY completed_at ensures we delete oldest jobs first.
+    // Active-root exclusion uses `NOT IN (SELECT ... unnest($3))` rather than
+    // `!= ALL($3)`: the subquery form lets the planner build a one-time hashed
+    // SubPlan and apply it as a filter on the ordered index scan, giving O(1)
+    // membership per candidate instead of a per-row linear array scan (which
+    // degrades sharply when many root jobs are active). The `u IS NOT NULL` guard
+    // sidesteps NOT IN's null-trap semantics ($3 holds non-null PK ids).
     let deleted_jobs: Vec<Uuid> = sqlx::query_scalar!(
         "DELETE FROM v2_job_completed
          WHERE id IN (
              SELECT jc.id FROM v2_job_completed jc
              LEFT JOIN v2_job j ON j.id = jc.id
              WHERE jc.completed_at <= now() - ($1::bigint::text || ' s')::interval
-               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) != ALL($3)
+               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) NOT IN (
+                   SELECT u FROM unnest($3::uuid[]) AS u WHERE u IS NOT NULL
+               )
              ORDER BY jc.completed_at ASC
              LIMIT $2
              FOR UPDATE OF jc SKIP LOCKED
diff --git a/backend/windmill-api-settings/src/log_cleanup.rs b/backend/windmill-api-settings/src/log_cleanup.rs
index 762a40e69d..2264e27037 100644
--- a/backend/windmill-api-settings/src/log_cleanup.rs
+++ b/backend/windmill-api-settings/src/log_cleanup.rs
@@ -395,13 +395,17 @@ async fn delete_expired_jobs_batch(
     .fetch_all(&mut *tx)
     .await?;
 
+    // Active-root exclusion via NOT IN (hashed SubPlan) instead of `!= ALL($3)`;
+    // see backend/src/monitor.rs::delete_expired_jobs_batch for the rationale.
     let deleted_jobs: Vec<Uuid> = sqlx::query_scalar!(
         "DELETE FROM v2_job_completed
          WHERE id IN (
              SELECT jc.id FROM v2_job_completed jc
              LEFT JOIN v2_job j ON j.id = jc.id
              WHERE jc.completed_at <= now() - ($1::bigint::text || ' s')::interval
-               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) != ALL($3)
+               AND COALESCE(j.root_job, j.flow_innermost_root_job, jc.id) NOT IN (
+                   SELECT u FROM unnest($3::uuid[]) AS u WHERE u IS NOT NULL
+               )
              ORDER BY jc.completed_at ASC
              LIMIT $2
              FOR UPDATE OF jc SKIP LOCKED