diff --git a/packages/cloudflare-runtime/src/rolldown/plugins/options.ts b/packages/cloudflare-runtime/src/rolldown/plugins/options.ts
index f325b084b9..1bb10f3147 100644
--- a/packages/cloudflare-runtime/src/rolldown/plugins/options.ts
+++ b/packages/cloudflare-runtime/src/rolldown/plugins/options.ts
@@ -248,6 +248,28 @@ export const optionsPlugin = createPlugin<"options", OptionsApi>(
             },
           };
         },
+        // Vite merges every plugin's `config` result into the config the next
+        // plugin sees, so the entry input returned above is UNIONED with an
+        // input the app's own plugins declared for the same environment — a
+        // framework that names its own server entry (Foldkit's `ssr.build`,
+        // for one) leaves two entry chunks in the bundle, and the deployed
+        // Worker becomes whichever one the bundle happens to list first.
+        // `main` names the Worker entry, so when it is set it replaces rather
+        // than joins. This hook runs per environment after config resolution,
+        // where nothing merges over it.
+        options(options) {
+          if (pluginOptions.main === undefined) return;
+          // Only the entry environment carries the Worker's input; children
+          // (e.g. an RSC build's `ssr`) keep the entries their framework gave
+          // them. Without a resolvable environment there is nothing to check
+          // against, so leave the options alone.
+          const environmentName = this.environment?.name;
+          if (environmentName === undefined) return;
+          if (environmentName !== parseViteEnvironments(pluginOptions)[0])
+            return;
+          options.input = wrapInput(input);
+          return options;
+        },
       },
     };
   },
diff --git a/packages/cloudflare-runtime/src/rolldown/test/worker-entry.test.ts b/packages/cloudflare-runtime/src/rolldown/test/worker-entry.test.ts
index b339be6b28..fe8104916c 100644
--- a/packages/cloudflare-runtime/src/rolldown/test/worker-entry.test.ts
+++ b/packages/cloudflare-runtime/src/rolldown/test/worker-entry.test.ts
@@ -47,4 +47,122 @@ describe("vite worker entry resolution", () => {
         "\0distilled:worker-entry:virtual:react-router/server-build",
     });
   });
+
+  // Vite's `runConfigHook` folds each plugin's result into the config the next
+  // plugin sees (`conf = mergeConfig(conf, res)`), so an app that declares its
+  // own server entry for the same environment ends up with both inputs in the
+  // merged config. The `options` hook is what makes `main` win.
+  const APP_DECLARED_SSR_INPUT: vite.UserConfig = {
+    root: "/project",
+    environments: {
+      ssr: {
+        build: {
+          rollupOptions: {
+            input: { "entry.server": "/src/entry.server.ts" },
+          },
+        },
+      },
+    },
+  };
+
+  const MAIN = "./src/worker.ts";
+
+  const callOptions = async (
+    environment: { name: string } | undefined,
+    input: unknown,
+    main: string | null = MAIN,
+  ) => {
+    const plugin = optionsPlugin.vite({
+      ...(main === null ? {} : { main }),
+      compatibilityDate: "2025-07-01",
+    });
+    assert(
+      typeof plugin.config === "function",
+      "plugin.config is not a function",
+    );
+    // Populates the plugin's resolved input, exactly as a real config pass does.
+    await plugin.config.call({ meta: {} } as never, APP_DECLARED_SSR_INPUT, {
+      command: "build",
+      mode: "production",
+    } as vite.ConfigEnv);
+    assert(
+      typeof plugin.options === "function",
+      "plugin.options is not a function",
+    );
+    const options = { input };
+    const returned = await plugin.options.call(
+      {
+        meta: {},
+        ...(environment === undefined ? {} : { environment }),
+      } as never,
+      options as never,
+    );
+    return (returned ?? options) as { input?: unknown };
+  };
+
+  const workerEntry = `\0distilled:worker-entry:${path
+    .resolve("/project", MAIN)
+    .replaceAll("\\", "/")}`;
+
+  it("merges the app's entry input with main before the build sees it", async () => {
+    const { mergeConfig } = await import("vite");
+    const plugin = optionsPlugin.vite({
+      main: MAIN,
+      compatibilityDate: "2025-07-01",
+    });
+    assert(
+      typeof plugin.config === "function",
+      "plugin.config is not a function",
+    );
+    const result = (await plugin.config.call(
+      { meta: {} } as never,
+      APP_DECLARED_SSR_INPUT,
+      { command: "build", mode: "production" } as vite.ConfigEnv,
+    )) as vite.UserConfig;
+
+    // Not the fix — the reason one is needed. Two entry chunks reach the
+    // bundle, and the deployed Worker is whichever the bundle lists first.
+    expect(
+      Object.keys(
+        mergeConfig(APP_DECLARED_SSR_INPUT, result).environments?.ssr?.build
+          ?.rollupOptions?.input as object,
+      ).sort(),
+    ).toEqual(["entry.server", "worker"]);
+  });
+
+  it("replaces an app-declared entry input with main", async () => {
+    const options = await callOptions(
+      { name: "ssr" },
+      {
+        "entry.server": "/src/entry.server.ts",
+        worker: workerEntry,
+      },
+    );
+
+    expect(options.input).toEqual({ worker: workerEntry });
+  });
+
+  it("leaves child environments alone", async () => {
+    const input = { "entry.server": "/src/entry.server.ts" };
+
+    const options = await callOptions({ name: "rsc" }, input);
+
+    expect(options.input).toEqual(input);
+  });
+
+  it("leaves the input alone when no main is declared", async () => {
+    const input = { "entry.server": "/src/entry.server.ts" };
+
+    const options = await callOptions({ name: "ssr" }, input, null);
+
+    expect(options.input).toEqual(input);
+  });
+
+  it("leaves the input alone without a resolvable environment", async () => {
+    const input = { "entry.server": "/src/entry.server.ts" };
+
+    const options = await callOptions(undefined, input);
+
+    expect(options.input).toEqual(input);
+  });
 });