diff --git a/.changeset/query-entities-inner-join.md b/.changeset/query-entities-inner-join.md
new file mode 100644
index 0000000000..ee4eb30863
--- /dev/null
+++ b/.changeset/query-entities-inner-join.md
@@ -0,0 +1,7 @@
+---
+'@backstage/plugin-catalog-backend': minor
+---
+
+**BREAKING**: When paginating entities with an order field via `/entities/by-query`, entities that lack the order field are now excluded from both the result set and the `totalItems` count. Previously these entities appeared at the end of the sorted result via `NULLS LAST`, but cursor-based pagination could not actually reach them past the first page — the count over-reported the number of navigable entities. The new behavior aligns the count with what is actually returned.
+
+This also removes the `DISTINCT` deduplication from the sort-field CTE, which is a prerequisite for the planner to use the `(key, value, entity_id)` index in sort order and short-circuit on `LIMIT`. Installations with duplicate search rows should land the search-table deduplication migration before adopting this change.
diff --git a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.test.ts b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.test.ts
index 427a9c8ce0..241af26541 100644
--- a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.test.ts
+++ b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.test.ts
@@ -1899,27 +1899,28 @@ describe('DefaultEntitiesCatalog', () => {
           stitcher,
         });
 
-        await expect(
-          catalog
-            .queryEntities({
-              orderFields: [{ field: 'metadata.title', order: 'asc' }],
-              credentials: mockCredentials.none(),
-            })
-            .then(r =>
-              entitiesResponseToObjects(r.items).map(e => e!.metadata.name),
-            ),
-        ).resolves.toEqual(['CC', 'BB', 'AA']); // 'AA' has no title, ends up last
+        // Entities without the sort field are excluded — sorting by a field
+        // means "show me entities that have this field, in order." The count
+        // also reflects only the entities that will be returned.
+        const ascResult = await catalog.queryEntities({
+          orderFields: [{ field: 'metadata.title', order: 'asc' }],
+          credentials: mockCredentials.none(),
+        });
+        expect(
+          entitiesResponseToObjects(ascResult.items).map(e => e!.metadata.name),
+        ).toEqual(['CC', 'BB']);
+        expect(ascResult.totalItems).toBe(2);
 
-        await expect(
-          catalog
-            .queryEntities({
-              orderFields: [{ field: 'metadata.title', order: 'desc' }],
-              credentials: mockCredentials.none(),
-            })
-            .then(r =>
-              entitiesResponseToObjects(r.items).map(e => e!.metadata.name),
-            ),
-        ).resolves.toEqual(['BB', 'CC', 'AA']); // 'AA' has no title, ends up last
+        const descResult = await catalog.queryEntities({
+          orderFields: [{ field: 'metadata.title', order: 'desc' }],
+          credentials: mockCredentials.none(),
+        });
+        expect(
+          entitiesResponseToObjects(descResult.items).map(
+            e => e!.metadata.name,
+          ),
+        ).toEqual(['BB', 'CC']);
+        expect(descResult.totalItems).toBe(2);
       },
     );
 
diff --git a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
index b5a65d6d05..35374cfd15 100644
--- a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
+++ b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
@@ -273,33 +273,39 @@ export class DefaultEntitiesCatalog implements EntitiesCatalog {
     const sortField = cursor.orderFields.at(0);
 
     // The first part of the query builder is a subquery that applies all of the
-    // filtering.
+    // filtering. When a sort field is specified, the search table for that key
+    // drives the query via INNER JOIN so that the (key, value, entity_id)
+    // index walks rows in sort order, letting LIMIT short-circuit. Entities
+    // that lack the sort field are excluded from both the result set and the
+    // count — this is a deliberate choice that aligns totalItems with the
+    // number of entities actually reachable through cursor pagination.
     const dbQuery = this.database.with(
       'filtered',
       ['entity_id', 'final_entity', ...(sortField ? ['value'] : [])],
       inner => {
-        inner
-          .from<DbFinalEntitiesRow>('final_entities')
-          .whereNotNull('final_entity');
-
         if (sortField) {
           inner
-            .distinct()
-            .leftOuterJoin('search', qb =>
-              qb
-                .on('search.entity_id', 'final_entities.entity_id')
-                .andOnVal('search.key', sortField.field),
+            .from('search')
+            .innerJoin(
+              'final_entities',
+              'final_entities.entity_id',
+              'search.entity_id',
             )
+            .where('search.key', sortField.field)
+            .whereNotNull('final_entities.final_entity')
             .select({
               entity_id: 'final_entities.entity_id',
               final_entity: 'final_entities.final_entity',
               value: 'search.value',
             });
         } else {
-          inner.select({
-            entity_id: 'final_entities.entity_id',
-            final_entity: 'final_entities.final_entity',
-          });
+          inner
+            .from<DbFinalEntitiesRow>('final_entities')
+            .whereNotNull('final_entity')
+            .select({
+              entity_id: 'final_entities.entity_id',
+              final_entity: 'final_entities.final_entity',
+            });
         }
 
         // Add regular filters and/or predicate query, if given