diff --git a/src/plugins/prerender-plugin.js b/src/plugins/prerender-plugin.js
index 36e1e98..051c740 100644
--- a/src/plugins/prerender-plugin.js
+++ b/src/plugins/prerender-plugin.js
@@ -72,6 +72,7 @@ function serializeElement(element) {
  * @returns {import('vite').Plugin}
  */
 export function prerenderPlugin({ prerenderScript, renderTarget, additionalPrerenderRoutes } = {}) {
+    const originalPrerenderScript = prerenderScript;
     let viteConfig = {};
     let userEnabledSourceMaps;
     let ssrBuild = false;
@@ -185,7 +186,12 @@ export function prerenderPlugin({ prerenderScript, renderTarget, additionalPrere
 
             config.build.rollupOptions.output ??= {};
             config.build.rollupOptions.output.manualChunks = (id) => {
-                if (id.includes(prerenderScript) || id.includes(preloadPolyfillId)) {
+                // If the user has specified a prerender script via the plugin options, we don't
+                // want to merge it into the index, but if they're using `<script prerender>` in their
+                // HTML, then we do.
+                //
+                // As such, we grab & store the original value & check against it here.
+                if ((!originalPrerenderScript && id.includes(prerenderScript)) || id.includes(preloadPolyfillId)) {
                     return 'index';
                 }
             };
diff --git a/tests/config.test.js b/tests/config.test.js
index 9829e89..b150e42 100644
--- a/tests/config.test.js
+++ b/tests/config.test.js
@@ -1,5 +1,7 @@
 import { test } from 'uvu';
 import * as assert from 'uvu/assert';
+import path from 'node:path';
+import { promises as fs } from 'node:fs';
 
 import { setupTest, teardownTest, loadFixture, viteBuild } from './lib/lifecycle.js';
 import { getOutputFile, outputFileExists, writeFixtureFile } from './lib/utils.js';
@@ -30,6 +32,12 @@ test('Should support the `prerenderScript` plugin option', async () => {
 
     const prerenderedHtml = await getOutputFile(env.tmp.path, 'index.html');
     assert.match(prerenderedHtml, '<body><h1>Hello, World!</h1>');
+
+    const outDirAssets = await fs.readdir(path.join(env.tmp.path, 'dist', 'assets'));
+
+    assert.equal(outDirAssets.length, 2);
+    assert.ok(outDirAssets.some(asset => /^index-/.test(asset)))
+    assert.ok(outDirAssets.some(asset => /^prerender-/.test(asset)))
 });
 
 test('Should throw if no `prerenderScript` is specified or can be found', async () => {
