diff --git a/crates/bevy_ecs/src/bundle/mod.rs b/crates/bevy_ecs/src/bundle/mod.rs
index b6a81ebd27328..f7cd9996b2853 100644
--- a/crates/bevy_ecs/src/bundle/mod.rs
+++ b/crates/bevy_ecs/src/bundle/mod.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 //! Types for handling [`Bundle`]s.
 //!
 //! This module contains the [`Bundle`] trait and some other helper types.
diff --git a/crates/bevy_ecs/src/entity/clone_entities.rs b/crates/bevy_ecs/src/entity/clone_entities.rs
index 0f7105e0eb0ce..824775fb7b4b0 100644
--- a/crates/bevy_ecs/src/entity/clone_entities.rs
+++ b/crates/bevy_ecs/src/entity/clone_entities.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 use crate::{
     archetype::Archetype,
     bundle::{Bundle, BundleRemover, InsertMode},
diff --git a/crates/bevy_ecs/src/lib.rs b/crates/bevy_ecs/src/lib.rs
index 4c8763ad66f64..4c336a562bb51 100644
--- a/crates/bevy_ecs/src/lib.rs
+++ b/crates/bevy_ecs/src/lib.rs
@@ -1,7 +1,3 @@
-#![expect(
-    unsafe_op_in_unsafe_fn,
-    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
-)]
 #![doc = include_str!("../README.md")]
 #![cfg_attr(
     any(docsrs, docsrs_dep),
diff --git a/crates/bevy_ecs/src/query/mod.rs b/crates/bevy_ecs/src/query/mod.rs
index b5c1b3d7d18a5..065eadd24db88 100644
--- a/crates/bevy_ecs/src/query/mod.rs
+++ b/crates/bevy_ecs/src/query/mod.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 //! Contains APIs for retrieving component data from the world.
 
 mod access;
diff --git a/crates/bevy_ecs/src/schedule/executor/multi_threaded.rs b/crates/bevy_ecs/src/schedule/executor/multi_threaded.rs
index 497b937c31f51..33bc8d0b80079 100644
--- a/crates/bevy_ecs/src/schedule/executor/multi_threaded.rs
+++ b/crates/bevy_ecs/src/schedule/executor/multi_threaded.rs
@@ -448,12 +448,21 @@ impl ExecutorState {
         }
 
         #[cfg(feature = "hotpatching")]
-        let hotpatch_tick = context
-            .environment
-            .world_cell
-            .get_resource_ref::<HotPatchChanges>()
-            .map(|r| r.last_changed())
-            .unwrap_or_default();
+        #[expect(
+            clippy::undocumented_unsafe_blocks,
+            reason = "This actually could result in UB if a system tries to mutate
+            `HotPatchChanges`. We allow this as the resource only exists with the `hotpatching` feature.
+            and `hotpatching` should never be enabled in release."
+        )]
+        #[cfg(feature = "hotpatching")]
+        let hotpatch_tick = unsafe {
+            context
+                .environment
+                .world_cell
+                .get_resource_ref::<HotPatchChanges>()
+        }
+        .map(|r| r.last_changed())
+        .unwrap_or_default();
 
         // can't borrow since loop mutably borrows `self`
         let mut ready_systems = core::mem::take(&mut self.ready_systems_copy);
diff --git a/crates/bevy_ecs/src/storage/mod.rs b/crates/bevy_ecs/src/storage/mod.rs
index 0584ae15c6738..084cca6bc8396 100644
--- a/crates/bevy_ecs/src/storage/mod.rs
+++ b/crates/bevy_ecs/src/storage/mod.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 //! Storage layouts for ECS data.
 //!
 //! This module implements the low-level collections that store data in a [`World`]. These all offer minimal and often
diff --git a/crates/bevy_ecs/src/system/combinator.rs b/crates/bevy_ecs/src/system/combinator.rs
index 0ef463fc45e0d..ad10d2ddd8cf6 100644
--- a/crates/bevy_ecs/src/system/combinator.rs
+++ b/crates/bevy_ecs/src/system/combinator.rs
@@ -167,8 +167,6 @@ where
             input: SystemIn<S>,
             world: &mut PrivateUnsafeWorldCell,
         ) -> Result<S::Out, RunSystemError> {
-            #![deny(unsafe_op_in_unsafe_fn)]
-
             // SAFETY: see comment on `Func::combine` call
             match (|| unsafe {
                 system.validate_param_unsafe(world.0)?;
diff --git a/crates/bevy_ecs/src/system/system_param.rs b/crates/bevy_ecs/src/system/system_param.rs
index 16af1523376e4..2a0498ffdcfdc 100644
--- a/crates/bevy_ecs/src/system/system_param.rs
+++ b/crates/bevy_ecs/src/system/system_param.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 pub use crate::change_detection::{NonSend, NonSendMut, Res, ResMut};
 use crate::{
     archetype::Archetypes,
diff --git a/crates/bevy_ecs/src/world/mod.rs b/crates/bevy_ecs/src/world/mod.rs
index a4f49c7460a35..3f39865f8f34d 100644
--- a/crates/bevy_ecs/src/world/mod.rs
+++ b/crates/bevy_ecs/src/world/mod.rs
@@ -1,3 +1,8 @@
+#![expect(
+    unsafe_op_in_unsafe_fn,
+    reason = "See #11590. To be removed once all applicable unsafe code has an unsafe block with a safety comment."
+)]
+
 //! Defines the [`World`] and APIs for accessing it directly.
 
 pub(crate) mod command_queue;