diff --git a/tests/fixtures/layouts/job-dedup-auto-shared-check.yaml b/tests/fixtures/layouts/job-dedup-auto-shared-check.yaml
new file mode 100644
index 0000000000..3f7ae48910
--- /dev/null
+++ b/tests/fixtures/layouts/job-dedup-auto-shared-check.yaml
@@ -0,0 +1,78 @@
+- queue:
+    name: integrated
+    allow-circular-dependencies: true
+
+- pipeline:
+    name: check
+    manager: independent
+    trigger:
+      gerrit:
+        - event: patchset-created
+    success:
+      gerrit:
+        Verified: 1
+    failure:
+      gerrit:
+        Verified: -1
+
+- pipeline:
+    name: gate
+    manager: dependent
+    success-message: Build succeeded (gate).
+    require:
+      gerrit:
+        approval:
+          - Approved: 1
+    trigger:
+      gerrit:
+        - event: comment-added
+          approval:
+            - Approved: 1
+    success:
+      gerrit:
+        Verified: 2
+        submit: true
+    failure:
+      gerrit:
+        Verified: -2
+    start:
+      gerrit:
+        Verified: 0
+    precedence: high
+
+- job:
+    name: base
+    parent: null
+    run: playbooks/run.yaml
+    nodeset:
+      nodes:
+        - label: debian
+          name: controller
+
+- job:
+    name: common-job
+    required-projects:
+      - org/project1
+      - org/project2
+
+- job:
+    name: project1-job
+
+- job:
+    name: project2-job
+
+- project:
+    name: org/project1
+    queue: integrated
+    check:
+      jobs:
+        - common-job
+        - project1-job
+
+- project:
+    name: org/project2
+    queue: integrated
+    check:
+      jobs:
+        - common-job
+        - project2-job
diff --git a/tests/unit/test_circular_dependencies.py b/tests/unit/test_circular_dependencies.py
index 25ce2b4c9b..72734bdad0 100644
--- a/tests/unit/test_circular_dependencies.py
+++ b/tests/unit/test_circular_dependencies.py
@@ -2206,6 +2206,55 @@ class TestGerritCircularDependencies(ZuulTestCase):
     def test_job_deduplication_semaphore_resources_first(self):
         self._test_job_deduplication_semaphore()
 
+    @simple_layout('layouts/job-dedup-auto-shared-check.yaml')
+    def test_job_deduplication_check(self):
+        self.executor_server.hold_jobs_in_build = True
+        A = self.fake_gerrit.addFakeChange('org/project1', 'master', 'A')
+        B = self.fake_gerrit.addFakeChange('org/project2', 'master', 'B')
+
+        # A <-> B
+        A.data["commitMessage"] = "{}\n\nDepends-On: {}\n".format(
+            A.subject, B.data["url"]
+        )
+        B.data["commitMessage"] = "{}\n\nDepends-On: {}\n".format(
+            B.subject, A.data["url"]
+        )
+
+        self.fake_gerrit.addEvent(A.getPatchsetCreatedEvent(1))
+        self.waitUntilSettled()
+        self.fake_gerrit.addEvent(B.getPatchsetCreatedEvent(1))
+        self.waitUntilSettled()
+
+        self.executor_server.release('common-job')
+        self.executor_server.release('project1-job')
+        self.waitUntilSettled()
+
+        # We do this even though it results in no changes to force an
+        # extra pipeline processing run to make sure we don't garbage
+        # collect the item early.
+        self.fake_gerrit.addEvent(B.getPatchsetCreatedEvent(1))
+        self.waitUntilSettled()
+
+        self.executor_server.release('project2-job')
+        self.waitUntilSettled()
+
+        self.assertHistory([
+            dict(name="project1-job", result="SUCCESS", changes="2,1 1,1"),
+            dict(name="common-job", result="SUCCESS", changes="2,1 1,1"),
+            dict(name="project2-job", result="SUCCESS", changes="1,1 2,1"),
+            # This is deduplicated
+            # dict(name="common-job", result="SUCCESS", changes="2,1 1,1"),
+        ], ordered=False)
+        self.assertEqual(len(self.fake_nodepool.history), 3)
+
+        # Make sure there are no leaked queue items
+        tenant = self.scheds.first.sched.abide.tenants.get("tenant-one")
+        pipeline = tenant.layout.pipelines["check"]
+        pipeline_path = pipeline.state.getPath()
+        all_items = set(self.zk_client.client.get_children(
+            f"{pipeline_path}/item"))
+        self.assertEqual(len(all_items), 0)
+
     def test_submitted_together(self):
         self.fake_gerrit._fake_submit_whole_topic = True
         A = self.fake_gerrit.addFakeChange('org/project1', "master", "A",
diff --git a/zuul/model.py b/zuul/model.py
index 566e7ec09e..1daf4d82aa 100644
--- a/zuul/model.py
+++ b/zuul/model.py
@@ -931,8 +931,19 @@ class PipelineState(zkobject.ZKObject):
         except NoNodeError:
             all_items = set()
 
-        known_items = {i.uuid for i in self._getKnownItems()}
-        stale_items = all_items - known_items
+        known_item_objs = self._getKnownItems()
+        known_items = {i.uuid for i in known_item_objs}
+        items_referenced_by_builds = set()
+        for i in known_item_objs:
+            build_set = i.current_build_set
+            job_graph = build_set.job_graph
+            if not job_graph:
+                continue
+            for job in job_graph.getJobs():
+                build = build_set.getBuild(job.name)
+                if build:
+                    items_referenced_by_builds.add(build.build_set.item.uuid)
+        stale_items = all_items - known_items - items_referenced_by_builds
         for item_uuid in stale_items:
             self.pipeline.manager.log.debug("Cleaning up stale item %s",
                                             item_uuid)
@@ -1273,16 +1284,14 @@ class ChangeQueue(zkobject.ZKObject):
                                          item_ahead=item.item_ahead)
 
         if item.bundle:
-            items_in_pipeline = self.pipeline.getAllItems(include_old=True)
-            if any([i in items_in_pipeline for i in item.bundle.items]):
-                item.updateAttributes(
-                    self.zk_context, item_ahead=None, items_behind=[],
-                    dequeue_time=time.time())
-            else:
-                # We no longer need the bundle items
-                for bundle_item in item.bundle.items:
-                    bundle_item.delete(self.zk_context)
-                item._set(dequeue_time=time.time())
+            # This item may have builds referenced by other items in
+            # the bundle, or even other bundles (in the case of
+            # independent pipelines).  Rather than trying to figure
+            # that out here, we will just let PipelineState.cleanup
+            # handle garbage collecting these items when done.
+            item.updateAttributes(
+                self.zk_context, item_ahead=None, items_behind=[],
+                dequeue_time=time.time())
         else:
             item.delete(self.zk_context)
             # We use the dequeue time for stats reporting, but the queue
@@ -5390,7 +5399,33 @@ class QueueItem(zkobject.ZKObject):
             ret = False
         return ret
 
-    def findDuplicateJob(self, job):
+    def findDuplicateBundles(self):
+        """
+        Find other bundles in the pipeline that are equivalent to ours.
+        """
+        if not self.bundle:
+            return None
+        ret = []
+        for item in self.queue.pipeline.getAllItems():
+            if not item.live:
+                continue
+            if item is self:
+                continue
+            if not item.bundle:
+                continue
+            other_bundle_changes = {i.change for i in item.bundle.items}
+            this_bundle_changes = {i.change for i in self.bundle.items}
+            if other_bundle_changes != this_bundle_changes:
+                continue
+            other_item_queue = {i.change for i in item.queue.queue}
+            this_item_queue = {i.change for i in self.queue.queue}
+            if other_item_queue != this_item_queue:
+                continue
+            if item.bundle not in ret:
+                ret.append(item.bundle)
+        return ret
+
+    def findDuplicateJob(self, job, other_bundles):
         """
         If another item in the bundle has a duplicate job,
         return the other item
@@ -5399,18 +5434,20 @@ class QueueItem(zkobject.ZKObject):
             return None
         if job.deduplicate is False:
             return None
-        for other_item in self.bundle.items:
-            if other_item is self:
-                continue
-            for other_job in other_item.getJobs():
-                if other_job.isEqual(job):
-                    if job.deduplicate == 'auto':
-                        # Deduplicate if there are required projects
-                        # or the item project is the same.
-                        if (not job.required_projects and
-                            self.change.project != other_item.change.project):
-                            continue
-                    return other_item
+        for other_bundle in other_bundles:
+            for other_item in other_bundle.items:
+                if other_item is self:
+                    continue
+                for other_job in other_item.getJobs():
+                    if other_job.isEqual(job):
+                        if job.deduplicate == 'auto':
+                            # Deduplicate if there are required projects
+                            # or the item project is the same.
+                            if (not job.required_projects and
+                                self.change.project !=
+                                other_item.change.project):
+                                continue
+                        return other_item
 
     def updateJobParentData(self):
         job_graph = self.current_build_set.job_graph
@@ -5506,6 +5543,13 @@ class QueueItem(zkobject.ZKObject):
 
         build_set = self.current_build_set
         job_graph = build_set.job_graph
+        if self.bundle and len([i for i in self.bundle.items if i.live]) > 1:
+            # We are in a queue that has multiple live items, so we
+            # will only check our own bundle.
+            other_bundles = [self.bundle]
+        else:
+            # Look for identical bundles elsewhere in the pipeline
+            other_bundles = self.findDuplicateBundles()
         for job in job_graph.getJobs():
             this_request = build_set.getJobNodeRequestID(job.name)
             this_nodeset = build_set.getJobNodeSetInfo(job.name)
@@ -5515,7 +5559,7 @@ class QueueItem(zkobject.ZKObject):
                 # Nothing more possible for this job
                 continue
 
-            other_item = self.findDuplicateJob(job)
+            other_item = self.findDuplicateJob(job, other_bundles)
             if not other_item:
                 continue
             other_build_set = other_item.current_build_set
diff --git a/zuul/scheduler.py b/zuul/scheduler.py
index 0ae736b017..da6d6a7702 100644
--- a/zuul/scheduler.py
+++ b/zuul/scheduler.py
@@ -2333,7 +2333,6 @@ class Scheduler(threading.Thread):
         pipeline.state.setDirty(self.zk_client.client)
         if pipeline.state.old_queues:
             self._reenqueuePipeline(tenant, pipeline, ctx)
-        pipeline.state.cleanup(ctx)
 
         with self.statsd_timer(f'{stats_key}.event_process'):
             self.process_pipeline_management_queue(tenant, pipeline)
@@ -2345,6 +2344,7 @@ class Scheduler(threading.Thread):
             with self.statsd_timer(f'{stats_key}.process'):
                 while not self._stopped and pipeline.manager.processQueue():
                     pass
+            pipeline.state.cleanup(ctx)
         except Exception:
             self.log.exception("Exception in pipeline processing:")
             pipeline._exception_count += 1