diff --git a/.changeset/fix-facets-perf-regression.md b/.changeset/fix-facets-perf-regression.md
new file mode 100644
index 0000000000..71f293271a
--- /dev/null
+++ b/.changeset/fix-facets-perf-regression.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-catalog-backend': patch
+---
+
+Fixed a performance regression in the `/entity-facets` endpoint when filters or permission conditions are applied, by routing the EXISTS-based filter through `final_entities` instead of correlating against the much larger `search` table.
diff --git a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
index 7fda0ac0f1..830120e486 100644
--- a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
+++ b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
@@ -690,13 +690,24 @@ export class DefaultEntitiesCatalog implements EntitiesCatalog {
       .groupBy(['search.key', 'search.original_value']);
 
     if (request.filter || request.query) {
+      // Build a subquery that finds matching entity IDs via
+      // final_entities, so that the EXISTS-based filters correlate
+      // against one-row-per-entity rather than the much larger search
+      // table. This keeps the facets aggregation fast even with many
+      // filter clauses or permission conditions.
+      const entityIdSubquery = this.database('final_entities')
+        .select('final_entities.entity_id')
+        .whereNotNull('final_entities.final_entity');
+
       applyEntityFilterToQuery({
         filter: request.filter,
         query: request.query,
-        targetQuery: query,
-        onEntityIdField: 'search.entity_id',
+        targetQuery: entityIdSubquery,
+        onEntityIdField: 'final_entities.entity_id',
         knex: this.database,
       });
+
+      query.whereIn('search.entity_id', entityIdSubquery);
     }
 
     const rows = await query;