diff --git a/mongoengine/fields.py b/mongoengine/fields.py
index b05e726a..8fdeae15 100644
--- a/mongoengine/fields.py
+++ b/mongoengine/fields.py
@@ -773,6 +773,9 @@ class EmbeddedDocumentField(BaseField):
 
     def prepare_query_value(self, op, value):
         if value is not None and not isinstance(value, self.document_type):
+            # Short circuit for special operators, returning them as is
+            if isinstance(value, dict) and all(k.startswith("$") for k in value.keys()):
+                return value
             try:
                 value = self.document_type._from_son(value)
             except ValueError:
diff --git a/tests/queryset/test_transform.py b/tests/queryset/test_transform.py
index 8d6c2d06..f5d248af 100644
--- a/tests/queryset/test_transform.py
+++ b/tests/queryset/test_transform.py
@@ -344,6 +344,31 @@ class TestTransform(unittest.TestCase):
         )
         assert update == {"$pull": {"content.text": {"word": {"$nin": ["foo", "bar"]}}}}
 
+    def test_transform_embedded_document_list_fields(self):
+        """
+        Test added to check filtering
+        EmbeddedDocumentListField which is inside a EmbeddedDocumentField
+        """
+
+        class Drink(EmbeddedDocument):
+            id = StringField()
+            meta = {"strict": False}
+
+        class Shop(Document):
+            drinks = EmbeddedDocumentListField(Drink)
+
+        Shop.drop_collection()
+        drinks = [Drink(id="drink_1"), Drink(id="drink_2")]
+        Shop.objects.create(drinks=drinks)
+        q_obj = transform.query(
+            Shop, drinks__all=[{"$elemMatch": {"_id": x.id}} for x in drinks]
+        )
+        assert q_obj == {
+            "drinks": {"$all": [{"$elemMatch": {"_id": x.id}} for x in drinks]}
+        }
+
+        Shop.drop_collection()
+
 
 if __name__ == "__main__":
     unittest.main()