diff --git a/pulp_container/app/tasks/sync_stages.py b/pulp_container/app/tasks/sync_stages.py
index 61b14ab5e..d8db3d515 100644
--- a/pulp_container/app/tasks/sync_stages.py
+++ b/pulp_container/app/tasks/sync_stages.py
@@ -12,6 +12,7 @@
 from pulpcore.plugin.stages import DeclarativeArtifact, DeclarativeContent, Stage, ContentSaver
 
 from pulp_container.constants import (
+    MANIFEST_TYPE,
     MEDIA_TYPE,
     SIGNATURE_API_EXTENSION_VERSION,
     SIGNATURE_HEADER,
@@ -287,9 +288,16 @@ async def resolve_flush(self):
         self.manifest_dcs.clear()
 
         for manifest_list_dc in self.manifest_list_dcs:
+            manifest_list_nature = MANIFEST_TYPE.UNKNOWN
             for listed_manifest in manifest_list_dc.extra_data["listed_manifests"]:
                 # Just await here. They will be associated in the post_save hook.
                 await listed_manifest["manifest_dc"].resolution()
+                if listed_manifest["manifest_dc"].content.type in [
+                    MANIFEST_TYPE.BOOTABLE,
+                    MANIFEST_TYPE.FLATPAK,
+                ]:
+                    manifest_list_nature = listed_manifest["manifest_dc"].content.type
+            manifest_list_dc.content.type = manifest_list_nature
             await self.put(manifest_list_dc)
         self.manifest_list_dcs.clear()
 
@@ -644,8 +652,10 @@ def _post_save(self, batch):
         if manifest_list_manifests:
             ManifestListManifest.objects.bulk_create(manifest_list_manifests, ignore_conflicts=True)
 
+        # DEPRECATED: is_bootable/is_flatpak are deprecated and will be removed in a future release.
+        # keeping this block for now to avoid introducing a bug or a regression
         # after creating the relation between listed manifests and manifest lists,
         # it is possible to initialize the nature of the corresponding manifest lists
         for ml in manifest_lists:
             if ml.init_manifest_list_nature():
-                ml.save(update_fields=["is_bootable", "is_flatpak", "type"])
+                ml.save(update_fields=["is_bootable", "is_flatpak"])