diff --git a/nixos/modules/system/activation/top-level.nix b/nixos/modules/system/activation/top-level.nix
index 896f8c0a6935..74ab7070fd0f 100644
--- a/nixos/modules/system/activation/top-level.nix
+++ b/nixos/modules/system/activation/top-level.nix
@@ -338,6 +338,12 @@ in
 
 
   config = {
+    assertions = [
+      {
+        assertion = config.system.copySystemConfiguration -> !lib.inPureEvalMode;
+        message = "system.copySystemConfiguration is not supported with flakes";
+      }
+    ];
 
     system.extraSystemBuilderCmds =
       optionalString