diff --git a/doc/classes/PhysicalBone3D.xml b/doc/classes/PhysicalBone3D.xml
index bce1a805269..ca1948e8e11 100644
--- a/doc/classes/PhysicalBone3D.xml
+++ b/doc/classes/PhysicalBone3D.xml
@@ -5,6 +5,7 @@
 	</brief_description>
 	<description>
 		The [PhysicalBone3D] node is a physics body that can be used to make bones in a [Skeleton3D] react to physics.
+		[b]Note:[/b] In order to detect physical bones with raycasts, the [member SkeletonModifier3D.active] property of the parent [PhysicalBoneSimulator3D] must be [code]true[/code] and the [Skeleton3D]'s bone must be assigned to [PhysicalBone3D] correctly; it means that [method get_bone_id] should return a valid id ([code]&gt;= 0[/code]).
 	</description>
 	<tutorials>
 	</tutorials>
diff --git a/doc/classes/Skeleton3D.xml b/doc/classes/Skeleton3D.xml
index 1167b70c8d2..5829a787a15 100644
--- a/doc/classes/Skeleton3D.xml
+++ b/doc/classes/Skeleton3D.xml
@@ -243,6 +243,8 @@
 			<return type="void" />
 			<param index="0" name="enabled" type="bool" />
 			<description>
+				This method exists for compatibility with old structures in which the [Skeleton3D] does not have a [PhysicalBoneSimulator3D] as a child, but directly has [PhysicalBone3D]s as children.
+				In case you need to raycast to it without running [method physical_bones_start_simulation], call this method with [code]enabled == true[/code].
 			</description>
 		</method>
 		<method name="set_bone_enabled">
diff --git a/scene/3d/physics/physical_bone_3d.cpp b/scene/3d/physics/physical_bone_3d.cpp
index c290f16c0d9..294690a89a0 100644
--- a/scene/3d/physics/physical_bone_3d.cpp
+++ b/scene/3d/physics/physical_bone_3d.cpp
@@ -764,7 +764,7 @@ void PhysicalBone3D::_notification(int p_what) {
 		case NOTIFICATION_EXIT_TREE: {
 			PhysicalBoneSimulator3D *simulator = get_simulator();
 			if (simulator) {
-				if (-1 != bone_id) {
+				if (bone_id != -1) {
 					simulator->unbind_physical_bone_from_bone(bone_id);
 					bone_id = -1;
 				}
@@ -816,7 +816,7 @@ void PhysicalBone3D::_body_state_changed(PhysicsDirectBodyState3D *p_state) {
 	PhysicalBoneSimulator3D *simulator = get_simulator();
 	Skeleton3D *skeleton = get_skeleton();
 	if (simulator && skeleton) {
-		if (-1 != bone_id) {
+		if (bone_id != -1) {
 			simulator->set_bone_global_pose(bone_id, skeleton->get_global_transform().affine_inverse() * (global_transform * body_offset_inverse));
 		}
 	}
@@ -1293,7 +1293,7 @@ void PhysicalBone3D::update_bone_id() {
 	const int new_bone_id = simulator->find_bone(bone_name);
 
 	if (new_bone_id != bone_id) {
-		if (-1 != bone_id) {
+		if (bone_id != -1) {
 			// Assert the unbind from old node
 			simulator->unbind_physical_bone_from_bone(bone_id);
 		}
@@ -1313,7 +1313,7 @@ void PhysicalBone3D::update_offset() {
 	Skeleton3D *skeleton = get_skeleton();
 	if (simulator && skeleton) {
 		Transform3D bone_transform(skeleton->get_global_transform());
-		if (-1 != bone_id) {
+		if (bone_id != -1) {
 			bone_transform *= simulator->get_bone_global_pose(bone_id);
 		}
 
@@ -1328,7 +1328,7 @@ void PhysicalBone3D::update_offset() {
 }
 
 void PhysicalBone3D::_start_physics_simulation() {
-	if (_internal_simulate_physics || !simulator_id.is_valid()) {
+	if (_internal_simulate_physics || !simulator_id.is_valid() || bone_id == -1) {
 		return;
 	}
 	reset_to_rest_position();
@@ -1344,7 +1344,7 @@ void PhysicalBone3D::_start_physics_simulation() {
 void PhysicalBone3D::_stop_physics_simulation() {
 	PhysicalBoneSimulator3D *simulator = get_simulator();
 	if (simulator) {
-		if (simulator->is_simulating_physics()) {
+		if (simulator->is_active() && bone_id != -1) {
 			set_body_mode(PhysicsServer3D::BODY_MODE_KINEMATIC);
 			PhysicsServer3D::get_singleton()->body_set_collision_layer(get_rid(), get_collision_layer());
 			PhysicsServer3D::get_singleton()->body_set_collision_mask(get_rid(), get_collision_mask());
diff --git a/scene/3d/skeleton_3d.cpp b/scene/3d/skeleton_3d.cpp
index 7c9fbd3b6de..b5263add48b 100644
--- a/scene/3d/skeleton_3d.cpp
+++ b/scene/3d/skeleton_3d.cpp
@@ -1140,7 +1140,8 @@ void Skeleton3D::set_animate_physical_bones(bool p_enabled) {
 	if (!sim) {
 		return;
 	}
-	sim->set_active(p_enabled);
+	animate_physical_bones = p_enabled;
+	sim->set_active(animate_physical_bones || sim->is_simulating_physics());
 }
 
 bool Skeleton3D::get_animate_physical_bones() const {
@@ -1148,7 +1149,7 @@ bool Skeleton3D::get_animate_physical_bones() const {
 	if (!sim) {
 		return false;
 	}
-	return sim->is_active();
+	return animate_physical_bones;
 }
 
 void Skeleton3D::physical_bones_stop_simulation() {
@@ -1157,7 +1158,7 @@ void Skeleton3D::physical_bones_stop_simulation() {
 		return;
 	}
 	sim->physical_bones_stop_simulation();
-	sim->set_active(false);
+	sim->set_active(animate_physical_bones || sim->is_simulating_physics());
 }
 
 void Skeleton3D::physical_bones_start_simulation_on(const TypedArray<StringName> &p_bones) {
diff --git a/scene/3d/skeleton_3d.h b/scene/3d/skeleton_3d.h
index eef7c9318d7..2d70aafcadb 100644
--- a/scene/3d/skeleton_3d.h
+++ b/scene/3d/skeleton_3d.h
@@ -67,6 +67,7 @@ class Skeleton3D : public Node3D {
 	GDCLASS(Skeleton3D, Node3D);
 
 #ifndef DISABLE_DEPRECATED
+	bool animate_physical_bones = false;
 	Node *simulator = nullptr;
 	void setup_simulator();
 #endif // _DISABLE_DEPRECATED