diff --git a/nixos/modules/misc/nixpkgs.nix b/nixos/modules/misc/nixpkgs.nix
index f9d8bccea284..1b0434fa7674 100644
--- a/nixos/modules/misc/nixpkgs.nix
+++ b/nixos/modules/misc/nixpkgs.nix
@@ -383,6 +383,16 @@ in
           the legacy definitions.
         '';
       }
+      {
+        assertion = opt.pkgs.isDefined -> cfg.config == {};
+        message = ''
+          Your system configures nixpkgs with an externally created instance.
+          `nixpkgs.config` options should be passed when creating the instance instead.
+
+          Current value:
+          ${lib.generators.toPretty { multiline = true; } opt.config}
+        '';
+      }
     ];
   };