diff --git a/airflow/jobs.py b/airflow/jobs.py
index 7e4867a770e25..c7cbcc7903897 100644
--- a/airflow/jobs.py
+++ b/airflow/jobs.py
@@ -571,8 +571,6 @@ def process_events(self, executor, dagbag):
                 # collect queued tasks for prioritiztion
                 if ti.state == State.QUEUED:
                     self.queued_tis.add(ti)
-                elif ti in self.queued_tis:
-                    self.queued_tis.remove(ti)
             else:
                 # special instructions for failed executions could go here
                 pass
@@ -601,6 +599,8 @@ def prioritize_queued(self, session, executor, dagbag):
             else:
                 d[ti.pool].append(ti)
 
+        self.queued_tis.clear()
+
         dag_blacklist = set(dagbag.paused_dags())
         for pool, tis in list(d.items()):
             if not pool:
diff --git a/tests/dags/test_issue_1225.py b/tests/dags/test_issue_1225.py
index 1c81bf0218f94..898cc04991eb9 100644
--- a/tests/dags/test_issue_1225.py
+++ b/tests/dags/test_issue_1225.py
@@ -115,3 +115,15 @@ def fail():
     subdag=subdag7)
 subdag7_task1.set_downstream(subdag7_task2)
 subdag7_task2.set_downstream(subdag7_task3)
+
+# DAG tests that queued tasks are run
+dag8 = DAG(
+    dag_id='test_scheduled_queued_tasks',
+    start_date=DEFAULT_DATE,
+    end_date=DEFAULT_DATE,
+    default_args=default_args)
+dag8_task1 = PythonOperator(
+    python_callable=fail,
+    task_id='test_queued_task',
+    dag=dag8,
+    pool='test_queued_pool')
diff --git a/tests/jobs.py b/tests/jobs.py
index 9f0070f6390d6..ac892404c362e 100644
--- a/tests/jobs.py
+++ b/tests/jobs.py
@@ -76,7 +76,7 @@ def run_with_timeout():
                 job.run()
         self.assertRaises(AirflowException, run_with_timeout)
 
-    def test_backfill_pooled_task(self):
+    def test_backfill_pooled_tasks(self):
         """
         Test that queued tasks are executed by BackfillJob
 
@@ -262,6 +262,35 @@ def test_dagrun_deadlock(self):
             dagrun_state=State.FAILED,
             advance_execution_date=True)
 
+    def test_scheduler_pooled_tasks(self):
+        """
+        Test that the scheduler handles queued tasks correctly
+        See issue #1299
+        """
+        session = settings.Session()
+        if not (
+                session.query(Pool)
+                .filter(Pool.pool == 'test_queued_pool')
+                .first()):
+            pool = Pool(pool='test_queued_pool', slots=5)
+            session.merge(pool)
+            session.commit()
+        session.close()
+
+        dag_id = 'test_scheduled_queued_tasks'
+        dag = self.dagbag.get_dag(dag_id)
+        dag.clear()
+
+        scheduler = SchedulerJob(dag_id, num_runs=10)
+        scheduler.run()
+
+        task_1 = dag.tasks[0]
+        ti = TI(task_1, dag.start_date)
+        ti.refresh_from_db()
+        self.assertEqual(ti.state, State.FAILED)
+
+        dag.clear()
+
     def test_dagrun_deadlock_ignore_depends_on_past_advance_ex_date(self):
         """
         DagRun is marked a success if ignore_first_depends_on_past=True