diff --git a/tests/fixtures/layouts/repo-checkout-no-timer-override.yaml b/tests/fixtures/layouts/repo-checkout-no-timer-override.yaml
new file mode 100644
index 0000000..de3bfe0
--- /dev/null
+++ b/tests/fixtures/layouts/repo-checkout-no-timer-override.yaml
@@ -0,0 +1,21 @@
+- pipeline:
+    name: periodic
+    manager: independent
+    # Trigger is required, set it to one that is a noop
+    # during tests that check the timer trigger.
+    trigger:
+      gerrit:
+        - event: ref-updated
+
+- job:
+    name: integration
+    branches: master
+    override-branch: stable/havana
+    required-projects:
+      - org/project1
+
+- project:
+    name: org/project1
+    periodic:
+      jobs:
+        - integration
diff --git a/tests/unit/test_executor.py b/tests/unit/test_executor.py
index 4700bd1..95cccee 100755
--- a/tests/unit/test_executor.py
+++ b/tests/unit/test_executor.py
@@ -274,8 +274,9 @@
         # Stop queuing timer triggered jobs so that the assertions
         # below don't race against more jobs being queued.
         self.commitConfigUpdate('common-config',
-                                'layouts/repo-checkout-no-timer.yaml')
+                                'layouts/repo-checkout-no-timer-override.yaml')
         self.sched.reconfigure(self.config)
+        self.waitUntilSettled()
 
         self.assertEquals(1, len(self.builds), "One build is running")
 
@@ -313,6 +314,7 @@
         self.commitConfigUpdate('common-config',
                                 'layouts/repo-checkout-no-timer.yaml')
         self.sched.reconfigure(self.config)
+        self.waitUntilSettled()
 
         self.assertEquals(2, len(self.builds), "Two builds are running")
 
diff --git a/tests/unit/test_scheduler.py b/tests/unit/test_scheduler.py
index 1e0affc..e36cdfe 100755
--- a/tests/unit/test_scheduler.py
+++ b/tests/unit/test_scheduler.py
@@ -1833,6 +1833,7 @@
         # Must be in same repo, so overwrite config with another one
         self.commitConfigUpdate('common-config', 'layouts/no-timer.yaml')
         self.sched.reconfigure(self.config)
+        self.waitUntilSettled()
 
         self.assertEqual(len(self.builds), 1, "One timer job")