diff --git a/src/libostree/ostree-repo-prune.c b/src/libostree/ostree-repo-prune.c
index 2d93a9cb..eca2cff6 100644
--- a/src/libostree/ostree-repo-prune.c
+++ b/src/libostree/ostree-repo-prune.c
@@ -303,10 +303,28 @@ ostree_repo_prune (OstreeRepo        *self,
       while (g_hash_table_iter_next (&hash_iter, &key, &value))
         {
           const char *checksum = value;
-          
-          if (!ostree_repo_traverse_commit_union (self, checksum, depth, data.reachable,
-                                            cancellable, error))
+          OstreeRepoCommitState commitstate;
+          GError *local_error = NULL;
+
+          if (!ostree_repo_load_commit (self, checksum, NULL, &commitstate,
+                                        error))
             goto out;
+
+          if (!ostree_repo_traverse_commit_union (self, checksum, depth, data.reachable,
+                                                  cancellable, &local_error))
+            {
+              /* Don't fail traversing a partial commit */
+              if ((commitstate & OSTREE_REPO_COMMIT_STATE_PARTIAL) > 0 &&
+                  g_error_matches (local_error, G_IO_ERROR, G_IO_ERROR_NOT_FOUND))
+                {
+                  g_clear_error (&local_error);
+                }
+              else
+                {
+                  g_propagate_error (error, local_error);
+                  goto out;
+                }
+            }
         }
     }
 
@@ -322,15 +340,33 @@ ostree_repo_prune (OstreeRepo        *self,
           GVariant *serialized_key = key;
           const char *checksum;
           OstreeObjectType objtype;
+          OstreeRepoCommitState commitstate;
+          GError *local_error = NULL;
 
           ostree_object_name_deserialize (serialized_key, &checksum, &objtype);
 
           if (objtype != OSTREE_OBJECT_TYPE_COMMIT)
             continue;
-          
-          if (!ostree_repo_traverse_commit_union (self, checksum, depth, data.reachable,
-                                                  cancellable, error))
+
+          if (!ostree_repo_load_commit (self, checksum, NULL, &commitstate,
+                                        error))
             goto out;
+
+          if (!ostree_repo_traverse_commit_union (self, checksum, depth, data.reachable,
+                                                  cancellable, &local_error))
+            {
+              /* Don't fail traversing a partial commit */
+              if ((commitstate & OSTREE_REPO_COMMIT_STATE_PARTIAL) > 0 &&
+                  g_error_matches (local_error, G_IO_ERROR, G_IO_ERROR_NOT_FOUND))
+                {
+                  g_clear_error (&local_error);
+                }
+              else
+                {
+                  g_propagate_error (error, local_error);
+                  goto out;
+                }
+            }
         }
     }