diff --git a/core/config/project_settings.cpp b/core/config/project_settings.cpp
index 078baf0e3ca..37e40c83783 100644
--- a/core/config/project_settings.cpp
+++ b/core/config/project_settings.cpp
@@ -1648,6 +1648,9 @@ ProjectSettings::ProjectSettings() {
 	GLOBAL_DEF("display/window/energy_saving/keep_screen_on", true);
 	GLOBAL_DEF("animation/warnings/check_invalid_track_paths", true);
 	GLOBAL_DEF("animation/warnings/check_angle_interpolation_type_conflicting", true);
+#ifndef DISABLE_DEPRECATED
+	GLOBAL_DEF_RST("animation/compatibility/default_parent_skeleton_in_mesh_instance_3d", false);
+#endif
 
 	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "audio/buses/default_bus_layout", PROPERTY_HINT_FILE, "*.tres"), "res://default_bus_layout.tres");
 	GLOBAL_DEF(PropertyInfo(Variant::INT, "audio/general/default_playback_type", PROPERTY_HINT_ENUM, "Stream,Sample"), 0);
diff --git a/doc/classes/MeshInstance3D.xml b/doc/classes/MeshInstance3D.xml
index 9bdab5b753c..edf6f0dd16c 100644
--- a/doc/classes/MeshInstance3D.xml
+++ b/doc/classes/MeshInstance3D.xml
@@ -128,8 +128,9 @@
 		<member name="mesh" type="Mesh" setter="set_mesh" getter="get_mesh">
 			The [Mesh] resource for the instance.
 		</member>
-		<member name="skeleton" type="NodePath" setter="set_skeleton_path" getter="get_skeleton_path" default="NodePath(&quot;..&quot;)">
+		<member name="skeleton" type="NodePath" setter="set_skeleton_path" getter="get_skeleton_path" default="NodePath(&quot;&quot;)">
 			[NodePath] to the [Skeleton3D] associated with the instance.
+			[b]Note:[/b] The default value of this property has changed in Godot 4.6. Enable [member ProjectSettings.animation/compatibility/default_parent_skeleton_in_mesh_instance_3d] if the old behavior is needed for compatibility.
 		</member>
 		<member name="skin" type="Skin" setter="set_skin" getter="get_skin">
 			The [Skin] to be used by this instance.
diff --git a/doc/classes/ProjectSettings.xml b/doc/classes/ProjectSettings.xml
index d74b67cae02..7a5ffe3199d 100644
--- a/doc/classes/ProjectSettings.xml
+++ b/doc/classes/ProjectSettings.xml
@@ -269,6 +269,9 @@
 		<member name="accessibility/general/updates_per_second" type="int" setter="" getter="" default="60">
 			The number of accessibility information updates per second.
 		</member>
+		<member name="animation/compatibility/default_parent_skeleton_in_mesh_instance_3d" type="bool" setter="" getter="" default="false">
+			If [code]true[/code], [member MeshInstance3D.skeleton] will point to the parent node ([code]..[/code]) by default, which was the behavior before Godot 4.6. It's recommended to keep this setting disabled unless the old behavior is needed for compatibility.
+		</member>
 		<member name="animation/warnings/check_angle_interpolation_type_conflicting" type="bool" setter="" getter="" default="true">
 			If [code]true[/code], [AnimationMixer] prints the warning of interpolation being forced to choose the shortest rotation path due to multiple angle interpolation types being mixed in the [AnimationMixer] cache.
 		</member>
diff --git a/scene/3d/mesh_instance_3d.cpp b/scene/3d/mesh_instance_3d.cpp
index 3c6f60f290a..e1378398fd3 100644
--- a/scene/3d/mesh_instance_3d.cpp
+++ b/scene/3d/mesh_instance_3d.cpp
@@ -926,6 +926,11 @@ void MeshInstance3D::_bind_methods() {
 
 MeshInstance3D::MeshInstance3D() {
 	_define_ancestry(AncestralClass::MESH_INSTANCE_3D);
+#ifndef DISABLE_DEPRECATED
+	if (use_parent_skeleton_compat) {
+		skeleton_path = NodePath("..");
+	}
+#endif
 }
 
 MeshInstance3D::~MeshInstance3D() {
diff --git a/scene/3d/mesh_instance_3d.h b/scene/3d/mesh_instance_3d.h
index 68c60b69b28..fe0f8993053 100644
--- a/scene/3d/mesh_instance_3d.h
+++ b/scene/3d/mesh_instance_3d.h
@@ -49,7 +49,7 @@ protected:
 	Ref<Skin> skin;
 	Ref<Skin> skin_internal;
 	Ref<SkinReference> skin_ref;
-	NodePath skeleton_path = NodePath("..");
+	NodePath skeleton_path;
 
 	LocalVector<float> blend_shape_tracks;
 	HashMap<StringName, int> blend_shape_properties;
@@ -73,6 +73,10 @@ protected:
 public:
 	static constexpr AncestralClass static_ancestral_class = AncestralClass::MESH_INSTANCE_3D;
 
+#ifndef DISABLE_DEPRECATED
+	static inline bool use_parent_skeleton_compat = false;
+#endif
+
 	void set_mesh(const Ref<Mesh> &p_mesh);
 	Ref<Mesh> get_mesh() const;
 
diff --git a/scene/register_scene_types.cpp b/scene/register_scene_types.cpp
index 0ecd1d2c4a3..f83a8de802b 100644
--- a/scene/register_scene_types.cpp
+++ b/scene/register_scene_types.cpp
@@ -607,6 +607,9 @@ void register_scene_types() {
 	GDREGISTER_CLASS(Camera3D);
 	GDREGISTER_CLASS(AudioListener3D);
 	GDREGISTER_CLASS(MeshInstance3D);
+#ifndef DISABLE_DEPRECATED
+	MeshInstance3D::use_parent_skeleton_compat = GLOBAL_GET("animation/compatibility/default_parent_skeleton_in_mesh_instance_3d");
+#endif
 	GDREGISTER_CLASS(OccluderInstance3D);
 	GDREGISTER_ABSTRACT_CLASS(Occluder3D);
 	GDREGISTER_CLASS(ArrayOccluder3D);