diff --git a/tests/runner-e2e/runner.spec.ts b/tests/runner-e2e/runner.spec.ts
index 4e341743f2..c23d36aa5a 100644
--- a/tests/runner-e2e/runner.spec.ts
+++ b/tests/runner-e2e/runner.spec.ts
@@ -803,12 +803,11 @@ for (const execution of executions) {
     });
 
     try {
-      const initialExperimental = await api.get<{
-        enableNativeRunner: boolean;
-      }>("/api/instance/settings/experimental");
-      expect(initialExperimental.enableNativeRunner).toBe(false);
+      // Each isolated campaign selects its generation explicitly; the app's
+      // default can change without changing which runtime this cell exercises.
+      const enableNativeRunner = execution.profile.generation === "native";
       await api.patch("/api/instance/settings/experimental", {
-        enableNativeRunner: true,
+        enableNativeRunner,
         ...(execution.task.flow === "warm_three_turn"
           ? { enableIsolatedWorkspaces: true }
           : {}),
@@ -818,6 +817,11 @@ for (const execution of executions) {
           : {}),
       });
 
+      const configuredExperimental = await api.get<{
+        enableNativeRunner: boolean;
+      }>("/api/instance/settings/experimental");
+      expect(configuredExperimental.enableNativeRunner).toBe(enableNativeRunner);
+
       fixtures = await setupLiveFixtures({
         api,
         execution,