diff --git a/core/io/missing_resource.cpp b/core/io/missing_resource.cpp
index c78195bc46c..1c15cc7dd38 100644
--- a/core/io/missing_resource.cpp
+++ b/core/io/missing_resource.cpp
@@ -74,6 +74,10 @@ bool MissingResource::is_recording_properties() const {
 	return recording_properties;
 }
 
+String MissingResource::get_save_class() const {
+	return original_class;
+}
+
 void MissingResource::_bind_methods() {
 	ClassDB::bind_method(D_METHOD("set_original_class", "name"), &MissingResource::set_original_class);
 	ClassDB::bind_method(D_METHOD("get_original_class"), &MissingResource::get_original_class);
diff --git a/core/io/missing_resource.h b/core/io/missing_resource.h
index f32d818ccb5..4cded5ca247 100644
--- a/core/io/missing_resource.h
+++ b/core/io/missing_resource.h
@@ -57,6 +57,8 @@ public:
 	void set_recording_properties(bool p_enable);
 	bool is_recording_properties() const;
 
+	virtual String get_save_class() const override;
+
 	MissingResource();
 };
 
diff --git a/core/io/resource_format_binary.cpp b/core/io/resource_format_binary.cpp
index b4826c356e0..bd54908d7b1 100644
--- a/core/io/resource_format_binary.cpp
+++ b/core/io/resource_format_binary.cpp
@@ -833,7 +833,7 @@ Error ResourceLoaderBinary::load() {
 			}
 
 			bool set_valid = true;
-			if (value.get_type() == Variant::OBJECT && missing_resource != nullptr) {
+			if (value.get_type() == Variant::OBJECT && missing_resource == nullptr && ResourceLoader::is_creating_missing_resources_if_class_unavailable_enabled()) {
 				// If the property being set is a missing resource (and the parent is not),
 				// then setting it will most likely not work.
 				// Instead, save it as metadata.
@@ -2220,10 +2220,10 @@ Error ResourceFormatSaverBinaryInstance::save(const String &p_path, const Ref<Re
 
 	List<ResourceData> resources;
 
-	Dictionary missing_resource_properties = p_resource->get_meta(META_MISSING_RESOURCES, Dictionary());
-
 	{
 		for (const Ref<Resource> &E : saved_resources) {
+			Dictionary missing_resource_properties = E->get_meta(META_MISSING_RESOURCES, Dictionary());
+
 			ResourceData &rd = resources.push_back(ResourceData())->get();
 			rd.type = _resource_get_class(E);
 
@@ -2238,7 +2238,7 @@ Error ResourceFormatSaverBinaryInstance::save(const String &p_path, const Ref<Re
 					continue;
 				}
 
-				if ((F.usage & PROPERTY_USAGE_STORAGE)) {
+				if ((F.usage & PROPERTY_USAGE_STORAGE) || missing_resource_properties.has(F.name)) {
 					Property p;
 					p.name_idx = get_string_index(F.name);
 
@@ -2253,7 +2253,7 @@ Error ResourceFormatSaverBinaryInstance::save(const String &p_path, const Ref<Re
 						p.value = E->get(F.name);
 					}
 
-					if (p.pi.type == Variant::OBJECT && missing_resource_properties.has(F.name)) {
+					if (F.type == Variant::OBJECT && missing_resource_properties.has(F.name)) {
 						// Was this missing resource overridden? If so do not save the old value.
 						Ref<Resource> res = p.value;
 						if (res.is_null()) {
diff --git a/scene/resources/packed_scene.cpp b/scene/resources/packed_scene.cpp
index d6fe4385c47..b6b2d92cdd9 100644
--- a/scene/resources/packed_scene.cpp
+++ b/scene/resources/packed_scene.cpp
@@ -786,7 +786,7 @@ Error SceneState::_parse_node(Node *p_owner, Node *p_node, int p_parent_idx, Has
 	Dictionary missing_resource_properties = p_node->get_meta(META_MISSING_RESOURCES, Dictionary());
 
 	for (const PropertyInfo &E : plist) {
-		if (!(E.usage & PROPERTY_USAGE_STORAGE)) {
+		if (!(E.usage & PROPERTY_USAGE_STORAGE) && !(missing_resource_properties.has(E.name))) {
 			continue;
 		}
 
diff --git a/scene/resources/resource_format_text.cpp b/scene/resources/resource_format_text.cpp
index d531eea3112..ceab1744596 100644
--- a/scene/resources/resource_format_text.cpp
+++ b/scene/resources/resource_format_text.cpp
@@ -600,7 +600,7 @@ Error ResourceLoaderText::load() {
 				if (do_assign) {
 					bool set_valid = true;
 
-					if (value.get_type() == Variant::OBJECT && missing_resource != nullptr) {
+					if (value.get_type() == Variant::OBJECT && missing_resource == nullptr && ResourceLoader::is_creating_missing_resources_if_class_unavailable_enabled()) {
 						// If the property being set is a missing resource (and the parent is not),
 						// then setting it will most likely not work.
 						// Instead, save it as metadata.
@@ -725,24 +725,25 @@ Error ResourceLoaderText::load() {
 			if (error) {
 				if (error != ERR_FILE_EOF) {
 					_printerr();
-				} else {
-					error = OK;
-					if (cache_mode != ResourceFormatLoader::CACHE_MODE_IGNORE) {
-						if (!ResourceCache::has(res_path)) {
-							resource->set_path(res_path);
-						}
-						resource->set_as_translation_remapped(translation_remapped);
-					} else {
-						resource->set_path_cache(res_path);
-					}
+					return error;
 				}
-				return error;
+				// EOF, Done parsing
+				error = OK;
+				if (cache_mode != ResourceFormatLoader::CACHE_MODE_IGNORE) {
+					if (!ResourceCache::has(res_path)) {
+						resource->set_path(res_path);
+					}
+					resource->set_as_translation_remapped(translation_remapped);
+				} else {
+					resource->set_path_cache(res_path);
+				}
+				break;
 			}
 
 			if (!assign.is_empty()) {
 				bool set_valid = true;
 
-				if (value.get_type() == Variant::OBJECT && missing_resource != nullptr) {
+				if (value.get_type() == Variant::OBJECT && ResourceLoader::is_creating_missing_resources_if_class_unavailable_enabled() && missing_resource == nullptr) {
 					// If the property being set is a missing resource (and the parent is not),
 					// then setting it will most likely not work.
 					// Instead, save it as metadata.
@@ -1914,7 +1915,7 @@ Error ResourceFormatSaverTextInstance::save(const String &p_path, const Ref<Reso
 				continue;
 			}
 
-			if (PE->get().usage & PROPERTY_USAGE_STORAGE) {
+			if (PE->get().usage & PROPERTY_USAGE_STORAGE || missing_resource_properties.has(PE->get().name)) {
 				String name = PE->get().name;
 				Variant value;
 				if (PE->get().usage & PROPERTY_USAGE_RESOURCE_NOT_PERSISTENT) {