diff --git a/crates/bevy_ecs/src/schedule/schedule.rs b/crates/bevy_ecs/src/schedule/schedule.rs
index c448093431aad..e6aa0eca0d1f1 100644
--- a/crates/bevy_ecs/src/schedule/schedule.rs
+++ b/crates/bevy_ecs/src/schedule/schedule.rs
@@ -271,7 +271,9 @@ impl Schedule {
     /// This prevents overflow and thus prevents false positives.
     pub(crate) fn check_change_ticks(&mut self, change_tick: Tick) {
         for system in &mut self.executable.systems {
-            system.check_change_tick(change_tick);
+            if !is_apply_deferred(system) {
+                system.check_change_tick(change_tick);
+            }
         }
 
         for conditions in &mut self.executable.system_conditions {