diff --git a/editor/animation_track_editor.cpp b/editor/animation_track_editor.cpp
index f5b5cfa848d..d1ac69c8d85 100644
--- a/editor/animation_track_editor.cpp
+++ b/editor/animation_track_editor.cpp
@@ -1274,12 +1274,7 @@ void AnimationTrackEdit::_notification(int p_what) {
 				}
 				text_color.a *= 0.7;
 			} else if (node) {
-				Ref<Texture> icon;
-				if (has_icon(node->get_class(), "EditorIcons")) {
-					icon = get_icon(node->get_class(), "EditorIcons");
-				} else {
-					icon = get_icon("Node", "EditorIcons");
-				}
+				Ref<Texture> icon = EditorNode::get_singleton()->get_object_icon(node, "Node");
 
 				draw_texture(icon, Point2(ofs, int(get_size().height - icon->get_height()) / 2));
 				icon_cache = icon;
@@ -3500,9 +3495,7 @@ void AnimationTrackEditor::_update_tracks() {
 				if (root && root->has_node(base_path)) {
 					Node *n = root->get_node(base_path);
 					if (n) {
-						if (has_icon(n->get_class(), "EditorIcons")) {
-							icon = get_icon(n->get_class(), "EditorIcons");
-						}
+						icon = EditorNode::get_singleton()->get_object_icon(n, "Node");
 						name = n->get_name();
 						tooltip = root->get_path_to(n);
 					}
diff --git a/editor/editor_data.cpp b/editor/editor_data.cpp
index 38f30df1694..f5846c10f64 100644
--- a/editor/editor_data.cpp
+++ b/editor/editor_data.cpp
@@ -499,7 +499,6 @@ Object *EditorData::instance_custom_type(const String &p_type, const String &p_i
 
 		for (int i = 0; i < get_custom_types()[p_inherits].size(); i++) {
 			if (get_custom_types()[p_inherits][i].name == p_type) {
-				Ref<Texture> icon = get_custom_types()[p_inherits][i].icon;
 				Ref<Script> script = get_custom_types()[p_inherits][i].script;
 
 				Object *ob = ClassDB::instance(p_inherits);
@@ -508,8 +507,6 @@ Object *EditorData::instance_custom_type(const String &p_type, const String &p_i
 					ob->call("set_name", p_type);
 				}
 				ob->set_script(script.get_ref_ptr());
-				if (icon.is_valid())
-					ob->set_meta("_editor_icon", icon);
 				return ob;
 			}
 		}
diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index 3183f1ae972..8bbfb388454 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -3488,6 +3488,69 @@ void EditorNode::stop_child_process() {
 	_menu_option_confirm(RUN_STOP, false);
 }
 
+Ref<Script> EditorNode::get_object_custom_type_base(const Object *p_object) const {
+	ERR_FAIL_COND_V(!p_object, NULL);
+
+	Ref<Script> script = p_object->get_script();
+
+	if (script.is_valid()) {
+		// Uncommenting would break things! Consider adding a parameter if you need it.
+		// StringName name = EditorNode::get_editor_data().script_class_get_name(base_script->get_path());
+		// if (name != StringName())
+		// 	return name;
+
+		// should probably be deprecated in 4.x
+		StringName base = script->get_instance_base_type();
+		if (base != StringName() && EditorNode::get_editor_data().get_custom_types().has(base)) {
+			const Vector<EditorData::CustomType> &types = EditorNode::get_editor_data().get_custom_types()[base];
+
+			Ref<Script> base_script = script;
+			while (base_script.is_valid()) {
+				for (int i = 0; i < types.size(); ++i) {
+					if (types[i].script == base_script) {
+						return types[i].script;
+					}
+				}
+				base_script = base_script->get_base_script();
+			}
+		}
+	}
+
+	return NULL;
+}
+
+StringName EditorNode::get_object_custom_type_name(const Object *p_object) const {
+	ERR_FAIL_COND_V(!p_object, StringName());
+
+	Ref<Script> script = p_object->get_script();
+	if (script.is_null() && p_object->is_class("Script")) {
+		script = p_object;
+	}
+
+	if (script.is_valid()) {
+		Ref<Script> base_script = script;
+		while (base_script.is_valid()) {
+			StringName name = EditorNode::get_editor_data().script_class_get_name(base_script->get_path());
+			if (name != StringName())
+				return name;
+
+			// should probably be deprecated in 4.x
+			StringName base = base_script->get_instance_base_type();
+			if (base != StringName() && EditorNode::get_editor_data().get_custom_types().has(base)) {
+				const Vector<EditorData::CustomType> &types = EditorNode::get_editor_data().get_custom_types()[base];
+				for (int i = 0; i < types.size(); ++i) {
+					if (types[i].script == base_script) {
+						return types[i].name;
+					}
+				}
+			}
+			base_script = base_script->get_base_script();
+		}
+	}
+
+	return StringName();
+}
+
 Ref<Texture> EditorNode::get_object_icon(const Object *p_object, const String &p_fallback) const {
 	ERR_FAIL_COND_V(!p_object || !gui_base, NULL);
 
@@ -3497,23 +3560,24 @@ Ref<Texture> EditorNode::get_object_icon(const Object *p_object, const String &p
 	}
 
 	if (script.is_valid()) {
-		StringName name = EditorNode::get_editor_data().script_class_get_name(script->get_path());
-		String icon_path = EditorNode::get_editor_data().script_class_get_icon_path(name);
-		if (icon_path.length())
-			return ResourceLoader::load(icon_path);
+		Ref<Script> base_script = script;
+		while (base_script.is_valid()) {
+			StringName name = EditorNode::get_editor_data().script_class_get_name(base_script->get_path());
+			String icon_path = EditorNode::get_editor_data().script_class_get_icon_path(name);
+			if (icon_path.length())
+				return ResourceLoader::load(icon_path);
 
-		// should probably be deprecated in 4.x
-		StringName base = script->get_instance_base_type();
-		if (base != StringName()) {
-			const Map<String, Vector<EditorData::CustomType> > &p_map = EditorNode::get_editor_data().get_custom_types();
-			for (const Map<String, Vector<EditorData::CustomType> >::Element *E = p_map.front(); E; E = E->next()) {
-				const Vector<EditorData::CustomType> &ct = E->value();
-				for (int i = 0; i < ct.size(); ++i) {
-					if (ct[i].name == base && ct[i].icon.is_valid()) {
-						return ct[i].icon;
+			// should probably be deprecated in 4.x
+			StringName base = base_script->get_instance_base_type();
+			if (base != StringName() && EditorNode::get_editor_data().get_custom_types().has(base)) {
+				const Vector<EditorData::CustomType> &types = EditorNode::get_editor_data().get_custom_types()[base];
+				for (int i = 0; i < types.size(); ++i) {
+					if (types[i].script == base_script && types[i].icon.is_valid()) {
+						return types[i].icon;
 					}
 				}
 			}
+			base_script = base_script->get_base_script();
 		}
 	}
 
diff --git a/editor/editor_node.h b/editor/editor_node.h
index 5dabe529f92..9aee19e6c19 100644
--- a/editor/editor_node.h
+++ b/editor/editor_node.h
@@ -776,6 +776,8 @@ public:
 	void stop_child_process();
 
 	Ref<Theme> get_editor_theme() const { return theme; }
+	Ref<Script> get_object_custom_type_base(const Object *p_object) const;
+	StringName get_object_custom_type_name(const Object *p_object) const;
 	Ref<Texture> get_object_icon(const Object *p_object, const String &p_fallback = "Object") const;
 	Ref<Texture> get_class_icon(const String &p_class, const String &p_fallback = "Object") const;
 
diff --git a/editor/scene_tree_dock.cpp b/editor/scene_tree_dock.cpp
index c43d1640789..a717b08d82f 100644
--- a/editor/scene_tree_dock.cpp
+++ b/editor/scene_tree_dock.cpp
@@ -466,8 +466,8 @@ void SceneTreeDock::_tool_selected(int p_tool, bool p_confirm_override) {
 
 				Node *n = Object::cast_to<Node>(selection[i]);
 				Ref<Script> existing = n->get_script();
-				if (existing.is_valid()) {
-					const RefPtr empty;
+				Ref<Script> empty = EditorNode::get_singleton()->get_object_custom_type_base(n);
+				if (existing != empty) {
 					editor_data->get_undo_redo().add_do_method(n, "set_script", empty);
 					editor_data->get_undo_redo().add_undo_method(n, "set_script", existing);
 				}
@@ -2329,6 +2329,7 @@ void SceneTreeDock::_tree_rmb(const Vector2 &p_menu_pos) {
 	menu->clear();
 
 	Ref<Script> existing_script;
+	bool exisiting_script_removable = true;
 	if (selection.size() == 1) {
 
 		Node *selected = selection[0];
@@ -2348,6 +2349,10 @@ void SceneTreeDock::_tree_rmb(const Vector2 &p_menu_pos) {
 		menu->add_separator();
 
 		existing_script = selected->get_script();
+
+		if (EditorNode::get_singleton()->get_object_custom_type_base(selected) == existing_script) {
+			exisiting_script_removable = false;
+		}
 	}
 
 	if (profile_allow_script_editing) {
@@ -2359,7 +2364,7 @@ void SceneTreeDock::_tree_rmb(const Vector2 &p_menu_pos) {
 				menu->add_icon_shortcut(get_icon("ScriptExtend", "EditorIcons"), ED_GET_SHORTCUT("scene_tree/extend_script"), TOOL_ATTACH_SCRIPT);
 			}
 		}
-		if (selection.size() > 1 || existing_script.is_valid()) {
+		if (selection.size() > 1 || (existing_script.is_valid() && exisiting_script_removable)) {
 			menu->add_icon_shortcut(get_icon("ScriptRemove", "EditorIcons"), ED_GET_SHORTCUT("scene_tree/clear_script"), TOOL_CLEAR_SCRIPT);
 		}
 		menu->add_separator();
diff --git a/editor/scene_tree_editor.cpp b/editor/scene_tree_editor.cpp
index c1a14685b0f..2d9accc3d85 100644
--- a/editor/scene_tree_editor.cpp
+++ b/editor/scene_tree_editor.cpp
@@ -212,13 +212,19 @@ bool SceneTreeEditor::_add_nodes(Node *p_node, TreeItem *p_parent) {
 		Color accent = get_color("accent_color", "Editor");
 
 		Ref<Script> script = p_node->get_script();
-		if (!script.is_null()) {
+		if (!script.is_null() && EditorNode::get_singleton()->get_object_custom_type_base(p_node) != script) {
 			//has script
 			item->add_button(0, get_icon("Script", "EditorIcons"), BUTTON_SCRIPT);
 		} else {
-			//has no script
+			//has no script (or script is a custom type)
 			item->set_custom_color(0, get_color("disabled_font_color", "Editor"));
 			item->set_selectable(0, false);
+
+			if (!script.is_null()) { // make sure to mark the script if a custom type
+				item->add_button(0, get_icon("Script", "EditorIcons"), BUTTON_SCRIPT);
+				item->set_button_disabled(0, item->get_button_count(0) - 1, true);
+			}
+
 			accent.a *= 0.7;
 		}
 
@@ -284,7 +290,10 @@ bool SceneTreeEditor::_add_nodes(Node *p_node, TreeItem *p_parent) {
 		item->add_button(0, get_icon("InstanceOptions", "EditorIcons"), BUTTON_SUBSCENE, false, TTR("Open in Editor"));
 		item->set_tooltip(0, TTR("Instance:") + " " + p_node->get_filename() + "\n" + TTR("Type:") + " " + p_node->get_class());
 	} else {
-		item->set_tooltip(0, String(p_node->get_name()) + "\n" + TTR("Type:") + " " + p_node->get_class());
+		StringName type = EditorNode::get_singleton()->get_object_custom_type_name(p_node);
+		if (type == StringName())
+			type = p_node->get_class();
+		item->set_tooltip(0, String(p_node->get_name()) + "\n" + TTR("Type:") + " " + type);
 	}
 
 	if (can_open_instance && undo_redo) { //Show buttons only when necessary(SceneTreeDock) to avoid crashes
@@ -295,6 +304,9 @@ bool SceneTreeEditor::_add_nodes(Node *p_node, TreeItem *p_parent) {
 		Ref<Script> script = p_node->get_script();
 		if (!script.is_null()) {
 			item->add_button(0, get_icon("Script", "EditorIcons"), BUTTON_SCRIPT, false, TTR("Open Script:") + " " + script->get_path());
+			if (EditorNode::get_singleton()->get_object_custom_type_base(p_node) == script) {
+				item->set_button_color(0, item->get_button_count(0) - 1, Color(1, 1, 1, 0.5));
+			}
 		}
 
 		if (p_node->is_class("CanvasItem")) {