diff --git a/common/flatpak-transaction.c b/common/flatpak-transaction.c
index 502602b3..cff57556 100644
--- a/common/flatpak-transaction.c
+++ b/common/flatpak-transaction.c
@@ -3982,7 +3982,7 @@ flatpak_transaction_real_run (FlatpakTransaction *self,
     {
       FlatpakTransactionOperation *op = l->data;
 
-      if (!add_deps (self, op, error))
+      if (!op->skip && !add_deps (self, op, error))
         return FALSE;
     }
 
@@ -3995,7 +3995,7 @@ flatpak_transaction_real_run (FlatpakTransaction *self,
     {
       FlatpakTransactionOperation *op = l->data;
 
-      if (!add_related (self, op, error))
+      if (!op->skip && !add_related (self, op, error))
         return FALSE;
     }