diff --git a/crates/bevy_ecs/src/schedule/schedule.rs b/crates/bevy_ecs/src/schedule/schedule.rs
index 584e621bf8..8015bde6c1 100644
--- a/crates/bevy_ecs/src/schedule/schedule.rs
+++ b/crates/bevy_ecs/src/schedule/schedule.rs
@@ -394,9 +394,21 @@ impl Schedule {
     }
 
     /// Changes miscellaneous build settings.
+    ///
+    /// If [`settings.auto_insert_apply_deferred`][ScheduleBuildSettings::auto_insert_apply_deferred]
+    /// is `false`, this clears `*_ignore_deferred` edge settings configured so far.
+    ///
+    /// Generally this method should be used before adding systems or set configurations to the schedule,
+    /// not after.
     pub fn set_build_settings(&mut self, settings: ScheduleBuildSettings) -> &mut Self {
         if settings.auto_insert_apply_deferred {
-            self.add_build_pass(passes::AutoInsertApplyDeferredPass::default());
+            if !self
+                .graph
+                .passes
+                .contains_key(&TypeId::of::<passes::AutoInsertApplyDeferredPass>())
+            {
+                self.add_build_pass(passes::AutoInsertApplyDeferredPass::default());
+            }
         } else {
             self.remove_build_pass::<passes::AutoInsertApplyDeferredPass>();
         }
@@ -2076,6 +2088,46 @@ mod tests {
     #[derive(Resource)]
     struct Resource2;
 
+    #[test]
+    fn unchanged_auto_insert_apply_deferred_has_no_effect() {
+        use alloc::{vec, vec::Vec};
+
+        #[derive(PartialEq, Debug)]
+        enum Entry {
+            System(usize),
+            SyncPoint(usize),
+        }
+
+        #[derive(Resource, Default)]
+        struct Log(Vec<Entry>);
+
+        fn system<const N: usize>(mut res: ResMut<Log>, mut commands: Commands) {
+            res.0.push(Entry::System(N));
+            commands
+                .queue(|world: &mut World| world.resource_mut::<Log>().0.push(Entry::SyncPoint(N)));
+        }
+
+        let mut world = World::default();
+        world.init_resource::<Log>();
+        let mut schedule = Schedule::default();
+        schedule.add_systems((system::<1>, system::<2>).chain_ignore_deferred());
+        schedule.set_build_settings(ScheduleBuildSettings {
+            auto_insert_apply_deferred: true,
+            ..Default::default()
+        });
+        schedule.run(&mut world);
+        let actual = world.remove_resource::<Log>().unwrap().0;
+
+        let expected = vec![
+            Entry::System(1),
+            Entry::System(2),
+            Entry::SyncPoint(1),
+            Entry::SyncPoint(2),
+        ];
+
+        assert_eq!(actual, expected);
+    }
+
     // regression test for https://github.com/bevyengine/bevy/issues/9114
     #[test]
     fn ambiguous_with_not_breaking_run_conditions() {