diff --git a/packages/plugin-vite/src/mod.ts b/packages/plugin-vite/src/mod.ts
index c49c244526c..b70433b58db 100644
--- a/packages/plugin-vite/src/mod.ts
+++ b/packages/plugin-vite/src/mod.ts
@@ -26,6 +26,91 @@ import { checkImports } from "./plugins/verify_imports.ts";
 import { isBuiltin } from "node:module";
 import { load as stdLoadEnv } from "@std/dotenv";
 import path from "node:path";
+import * as fs from "node:fs";
+
+// Packages that must always be bundled in the SSR build to avoid
+// duplicate module instances (e.g. preact's component registry).
+const SSR_BUNDLE_ALLOWLIST = new Set([
+  "preact",
+  "preact/hooks",
+  "preact/compat",
+  "preact/jsx-runtime",
+  "preact/jsx-dev-runtime",
+  "preact/test-utils",
+  "preact/debug",
+  "preact/devtools",
+  "@preact/signals",
+  "@preact/signals-core",
+]);
+
+/**
+ * Scan node_modules for CJS-only packages and return their names.
+ * A package is CJS-only if it has no ESM entry point (no "type": "module",
+ * no "module" field, no "import" condition in "exports").
+ */
+function findCjsOnlyPackages(root: string): string[] {
+  const result: string[] = [];
+  const nodeModulesDir = path.join(root, "node_modules");
+
+  let entries: fs.Dirent[];
+  try {
+    entries = fs.readdirSync(nodeModulesDir, { withFileTypes: true });
+  } catch {
+    return result;
+  }
+
+  for (const entry of entries) {
+    if (!entry.isDirectory() && !entry.isSymbolicLink()) continue;
+
+    if (entry.name.startsWith("@")) {
+      // Scoped package — check subdirectories
+      const scopeDir = path.join(nodeModulesDir, entry.name);
+      let scopeEntries: fs.Dirent[];
+      try {
+        scopeEntries = fs.readdirSync(scopeDir, { withFileTypes: true });
+      } catch {
+        continue;
+      }
+      for (const scopeEntry of scopeEntries) {
+        if (!scopeEntry.isDirectory() && !scopeEntry.isSymbolicLink()) {
+          continue;
+        }
+        const packageName = `${entry.name}/${scopeEntry.name}`;
+        if (isCjsOnly(nodeModulesDir, packageName)) {
+          result.push(packageName);
+        }
+      }
+    } else if (entry.name.startsWith(".")) {
+      continue;
+    } else {
+      if (isCjsOnly(nodeModulesDir, entry.name)) {
+        result.push(entry.name);
+      }
+    }
+  }
+
+  return result;
+}
+
+function isCjsOnly(nodeModulesDir: string, packageName: string): boolean {
+  if (SSR_BUNDLE_ALLOWLIST.has(packageName)) return false;
+
+  const pkgJsonPath = path.join(nodeModulesDir, packageName, "package.json");
+  try {
+    const pkg = JSON.parse(fs.readFileSync(pkgJsonPath, "utf-8"));
+    if (pkg.type === "module") return false;
+    if (pkg.module) return false;
+    if (pkg.exports) {
+      const exportsStr = JSON.stringify(pkg.exports);
+      if (exportsStr.includes('"import"')) return false;
+    }
+    // Must have a main entry (otherwise it's not a real package)
+    if (!pkg.main && !pkg.exports) return false;
+    return true;
+  } catch {
+    return false;
+  }
+}
 
 export type { FreshViteConfig };
 export type {
@@ -82,6 +167,7 @@ export function fresh(config?: FreshViteConfig): Plugin[] {
   });
 
   let isDev = false;
+  let resolvedRoot = process.cwd();
 
   const plugins: Plugin[] = [
     {
@@ -89,6 +175,16 @@ export function fresh(config?: FreshViteConfig): Plugin[] {
       sharedDuringBuild: true,
       config(config, env) {
         isDev = env.command === "serve";
+        resolvedRoot = config.root ? path.resolve(config.root) : process.cwd();
+
+        // Scan node_modules for CJS-only packages to externalize
+        // in the SSR build.
+        const cjsPackages = findCjsOnlyPackages(resolvedRoot);
+        const cjsExternalList = cjsPackages.map((pkg) =>
+          new RegExp(
+            `^${pkg.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}(\\/.*)?$`,
+          )
+        );
 
         return {
           server: {
@@ -178,6 +274,12 @@ export function fresh(config?: FreshViteConfig): Plugin[] {
                     : null) ??
                   "_fresh/server",
                 rollupOptions: {
+                  // Externalize CJS-only npm packages so they're
+                  // loaded at runtime by Deno's Node compat layer.
+                  // This avoids the CJS-to-ESM transform that can
+                  // cause TDZ errors when Rollup reorders bundled
+                  // declarations.
+                  external: cjsExternalList,
                   onwarn(warning, handler) {
                     // Ignore "use client"; warnings
                     if (warning.code === "MODULE_LEVEL_DIRECTIVE") {
diff --git a/packages/plugin-vite/tests/build_test.ts b/packages/plugin-vite/tests/build_test.ts
index 6fc9ec823b6..7350ec7b09b 100644
--- a/packages/plugin-vite/tests/build_test.ts
+++ b/packages/plugin-vite/tests/build_test.ts
@@ -13,6 +13,7 @@ import {
   usingEnv,
 } from "./test_utils.ts";
 import * as path from "@std/path";
+import { walk } from "@std/fs/walk";
 
 const viteResult = await buildVite(DEMO_DIR);
 
@@ -656,3 +657,49 @@ integrationTest(
     );
   },
 );
+
+// Issue: https://github.com/denoland/fresh/issues/3653
+integrationTest(
+  "vite build - CJS-only dependencies are externalized in SSR",
+  async () => {
+    const cjsFixture = path.join(FIXTURE_DIR, "cjs_dependency");
+    const result = await buildVite(cjsFixture);
+
+    // Read all server build files to verify the CJS module is externalized
+    // (appears as an external import, not inlined)
+    const serverDir = path.join(result.tmp, "_fresh", "server");
+    let allServerCode = "";
+    for await (
+      const entry of walk(serverDir, {
+        exts: [".mjs", ".js"],
+        includeFiles: true,
+        includeDirs: false,
+      })
+    ) {
+      allServerCode += await Deno.readTextFile(entry.path);
+    }
+
+    // The CJS module should be externalized — its implementation
+    // should NOT be inlined. The bundle should reference it as an
+    // external import.
+    expect(allServerCode).not.toContain("str.toUpperCase()");
+    expect(allServerCode).toContain("cjs-test-module");
+
+    // Symlink node_modules so the externalized import resolves at runtime
+    await Deno.symlink(
+      path.join(cjsFixture, "node_modules"),
+      path.join(result.tmp, "node_modules"),
+    );
+
+    // Verify the built server actually works with the externalized CJS dep
+    await launchProd(
+      { cwd: result.tmp },
+      async (address) => {
+        const res = await fetch(address);
+        const text = await res.text();
+        expect(text).toContain("HELLO, FRESH!");
+        expect(text).toContain("1.0.0");
+      },
+    );
+  },
+);
diff --git a/packages/plugin-vite/tests/fixtures/cjs_dependency/main.ts b/packages/plugin-vite/tests/fixtures/cjs_dependency/main.ts
new file mode 100644
index 00000000000..e5cf428a2cd
--- /dev/null
+++ b/packages/plugin-vite/tests/fixtures/cjs_dependency/main.ts
@@ -0,0 +1,5 @@
+import { App, staticFiles } from "@fresh/core";
+
+export const app = new App()
+  .use(staticFiles())
+  .fsRoutes();
diff --git a/packages/plugin-vite/tests/fixtures/cjs_dependency/routes/index.tsx b/packages/plugin-vite/tests/fixtures/cjs_dependency/routes/index.tsx
new file mode 100644
index 00000000000..d69b835c8d2
--- /dev/null
+++ b/packages/plugin-vite/tests/fixtures/cjs_dependency/routes/index.tsx
@@ -0,0 +1,12 @@
+import type { FreshContext } from "@fresh/core";
+// deno-lint-ignore no-external-import
+import { greet, version } from "cjs-test-module";
+
+export default function Home(_ctx: FreshContext) {
+  return (
+    <div>
+      <p class="greeting">{greet("Fresh")}</p>
+      <p class="version">{version}</p>
+    </div>
+  );
+}
diff --git a/packages/plugin-vite/tests/fixtures/cjs_dependency/vite.config.ts b/packages/plugin-vite/tests/fixtures/cjs_dependency/vite.config.ts
new file mode 100644
index 00000000000..727d49a2772
--- /dev/null
+++ b/packages/plugin-vite/tests/fixtures/cjs_dependency/vite.config.ts
@@ -0,0 +1,6 @@
+import { defineConfig } from "vite";
+import { fresh } from "@fresh/plugin-vite";
+
+export default defineConfig({
+  plugins: [fresh()],
+});