diff --git a/core/object/script_language.cpp b/core/object/script_language.cpp
index d2fc7392c86..c5856a8a81d 100644
--- a/core/object/script_language.cpp
+++ b/core/object/script_language.cpp
@@ -191,7 +191,17 @@ void Script::reload_from_file() {
 	set_source_code(rel->get_source_code());
 	set_last_modified_time(rel->get_last_modified_time());
 
-	reload();
+	// Only reload the script when there are no compilation errors to prevent printing the error messages twice.
+	if (rel->is_valid()) {
+		if (Engine::get_singleton()->is_editor_hint() && is_tool()) {
+			get_language()->reload_tool_script(this, true);
+		} else {
+			// It's important to set p_keep_state to true in order to manage reloading scripts
+			// that are currently instantiated.
+			reload(true);
+		}
+	}
+
 #else
 	Resource::reload_from_file();
 #endif
diff --git a/core/object/script_language.h b/core/object/script_language.h
index d0023d70e8c..3ddfbb3e7d3 100644
--- a/core/object/script_language.h
+++ b/core/object/script_language.h
@@ -112,7 +112,10 @@ class Script : public Resource {
 	OBJ_SAVE_TYPE(Script);
 
 protected:
-	virtual bool editor_can_reload_from_file() override { return false; } // this is handled by editor better
+	// Scripts are reloaded via the Script Editor when edited in Godot,
+	// the LSP server when edited in a connected external editor, or
+	// through EditorFileSystem::_update_script_documentation when updated directly on disk.
+	virtual bool editor_can_reload_from_file() override { return false; }
 	void _notification(int p_what);
 	static void _bind_methods();
 
diff --git a/editor/editor_file_system.cpp b/editor/editor_file_system.cpp
index adae6599c17..2b51071b150 100644
--- a/editor/editor_file_system.cpp
+++ b/editor/editor_file_system.cpp
@@ -1974,18 +1974,16 @@ void EditorFileSystem::_update_script_documentation() {
 		for (int i = 0; i < ScriptServer::get_language_count(); i++) {
 			ScriptLanguage *lang = ScriptServer::get_language(i);
 			if (lang->supports_documentation() && efd->files[index]->type == lang->get_type()) {
-				// Reloading the script from disk if resource already in memory. Otherwise, the
-				// ResourceLoader::load will return the last loaded version of the script (without the modifications).
-				// The only have the script already loaded here is to edit the script outside the
-				// editor without being connected to the LSP server.
-				Ref<Resource> res = ResourceCache::get_ref(path);
-				if (res.is_valid()) {
-					res->reload_from_file();
-				}
+				bool should_reload_script = _should_reload_script(path);
 				Ref<Script> scr = ResourceLoader::load(path);
 				if (scr.is_null()) {
 					continue;
 				}
+				if (should_reload_script) {
+					// Reloading the script from disk. Otherwise, the ResourceLoader::load will
+					// return the last loaded version of the script (without the modifications).
+					scr->reload_from_file();
+				}
 				Vector<DocData::ClassDoc> docs = scr->get_documentation();
 				for (int j = 0; j < docs.size(); j++) {
 					EditorHelp::get_doc_data()->add_doc(docs[j]);
@@ -2007,6 +2005,25 @@ void EditorFileSystem::_update_script_documentation() {
 	update_script_paths_documentation.clear();
 }
 
+bool EditorFileSystem::_should_reload_script(const String &p_path) {
+	if (first_scan) {
+		return false;
+	}
+
+	Ref<Script> scr = ResourceCache::get_ref(p_path);
+	if (scr.is_null()) {
+		// Not a script or not already loaded.
+		return false;
+	}
+
+	// Scripts are reloaded via the script editor if they are currently opened.
+	if (ScriptEditor::get_singleton()->get_open_scripts().has(scr)) {
+		return false;
+	}
+
+	return true;
+}
+
 void EditorFileSystem::_process_update_pending() {
 	_update_script_classes();
 	// Parse documentation second, as it requires the class names to be loaded
diff --git a/editor/editor_file_system.h b/editor/editor_file_system.h
index e02127cb13c..e53187c1d75 100644
--- a/editor/editor_file_system.h
+++ b/editor/editor_file_system.h
@@ -295,6 +295,7 @@ class EditorFileSystem : public Node {
 	void _update_script_documentation();
 	void _process_update_pending();
 	void _process_removed_files(const HashSet<String> &p_processed_files);
+	bool _should_reload_script(const String &p_path);
 
 	Mutex update_scene_mutex;
 	HashSet<String> update_scene_paths;
diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index 2b4b6a5b7ee..44292b41859 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -926,11 +926,7 @@ void EditorNode::_resources_changed(const Vector<String> &p_resources) {
 		}
 
 		if (!res->editor_can_reload_from_file()) {
-			Ref<Script> scr = res;
-			// Scripts are reloaded via the script editor.
-			if (scr.is_null() || ScriptEditor::get_singleton()->get_open_scripts().has(scr)) {
-				continue;
-			}
+			continue;
 		}
 		if (!res->get_path().is_resource_file() && !res->get_path().is_absolute_path()) {
 			continue;
diff --git a/editor/plugins/script_editor_plugin.cpp b/editor/plugins/script_editor_plugin.cpp
index 9579388d467..54730ec6743 100644
--- a/editor/plugins/script_editor_plugin.cpp
+++ b/editor/plugins/script_editor_plugin.cpp
@@ -1483,7 +1483,7 @@ void ScriptEditor::_menu_option(int p_option) {
 
 				current->apply_code();
 
-				Error err = scr->reload(false); // Always hard reload the script before running.
+				Error err = scr->reload(true); // Always hard reload the script before running.
 				if (err != OK || !scr->is_valid()) {
 					EditorToaster::get_singleton()->popup_str(TTR("Cannot run the script because it contains errors, check the output log."), EditorToaster::SEVERITY_WARNING);
 					return;