diff --git a/.changeset/init-trailing-newline.md b/.changeset/init-trailing-newline.md
new file mode 100644
index 000000000..29ce4f63c
--- /dev/null
+++ b/.changeset/init-trailing-newline.md
@@ -0,0 +1,5 @@
+---
+"clerk": patch
+---
+
+Keep the trailing newline on files that `clerk init` edits, so they no longer show "No newline at end of file" in `git diff`.
diff --git a/packages/cli-core/src/commands/init/frameworks/astro.test.ts b/packages/cli-core/src/commands/init/frameworks/astro.test.ts
index f6d7dd18f..00e87a6c2 100644
--- a/packages/cli-core/src/commands/init/frameworks/astro.test.ts
+++ b/packages/cli-core/src/commands/init/frameworks/astro.test.ts
@@ -64,6 +64,7 @@ export default defineConfig({
   if (config.type === "modify") {
     expect(config.content).toContain("clerk");
     expect(config.content).toContain("@clerk/astro");
+    expect(config.content.endsWith("\n")).toBe(true);
   }
 
   const mw = findAction(plan.actions, "src/middleware.ts");
diff --git a/packages/cli-core/src/commands/init/frameworks/astro.ts b/packages/cli-core/src/commands/init/frameworks/astro.ts
index 2d37b2be4..72a74d6e8 100644
--- a/packages/cli-core/src/commands/init/frameworks/astro.ts
+++ b/packages/cli-core/src/commands/init/frameworks/astro.ts
@@ -8,6 +8,7 @@ import {
   hasTailwindStyles,
   headerHtmlBlock,
   htmlAuthComponentMarkup,
+  printModule,
   scaffoldAuthFiles,
   scaffoldConfigFile,
   scaffoldEnvVars,
@@ -38,7 +39,7 @@ function addClerkImport(content: string): string {
   try {
     const mod = parseModule(content);
     mod.imports.$add({ from: "@clerk/astro", imported: "default", local: "clerk" });
-    return mod.generate().code;
+    return printModule(mod, content);
   } catch {
     return `import clerk from "@clerk/astro";\n${content}`;
   }
@@ -53,7 +54,7 @@ function addClerkToIntegrationsViaAst(content: string): string | null {
     if (!Array.isArray(defaultExport.integrations)) return null;
 
     defaultExport.integrations.push(builders.raw("clerk()"));
-    return mod.generate().code;
+    return printModule(mod, content);
   } catch {
     return null;
   }
diff --git a/packages/cli-core/src/commands/init/frameworks/helpers.ts b/packages/cli-core/src/commands/init/frameworks/helpers.ts
index acefea1d9..a18a6360b 100644
--- a/packages/cli-core/src/commands/init/frameworks/helpers.ts
+++ b/packages/cli-core/src/commands/init/frameworks/helpers.ts
@@ -14,6 +14,7 @@ export {
   hasClerkImport,
   indentBlock,
   safeAddImport,
+  printModule,
   insertAfterLastImport,
   addSuspenseImport,
   wrapBodyWithProvider,
diff --git a/packages/cli-core/src/commands/init/frameworks/nextjs-app.test.ts b/packages/cli-core/src/commands/init/frameworks/nextjs-app.test.ts
index 73625e503..fea0c0196 100644
--- a/packages/cli-core/src/commands/init/frameworks/nextjs-app.test.ts
+++ b/packages/cli-core/src/commands/init/frameworks/nextjs-app.test.ts
@@ -801,7 +801,8 @@ export default function RootLayout({ children }: { children: React.ReactNode })
       </body>
     </html>
   );
-}`,
+}
+`,
   });
 });
 
diff --git a/packages/cli-core/src/commands/init/frameworks/nuxt.test.ts b/packages/cli-core/src/commands/init/frameworks/nuxt.test.ts
index c09c347dc..376611a41 100644
--- a/packages/cli-core/src/commands/init/frameworks/nuxt.test.ts
+++ b/packages/cli-core/src/commands/init/frameworks/nuxt.test.ts
@@ -61,6 +61,7 @@ test("scaffolds all actions for a fresh Nuxt project (Nuxt 3 layout)", async ()
   expect(config.type).toBe("modify");
   if (config.type === "modify") {
     expect(config.content).toContain("@clerk/nuxt");
+    expect(config.content.endsWith("\n")).toBe(true);
   }
 
   // Nuxt 3 layout: pages at pages/ (no app/ directory)
diff --git a/packages/cli-core/src/commands/init/frameworks/nuxt.ts b/packages/cli-core/src/commands/init/frameworks/nuxt.ts
index e0ec0a417..3a1575811 100644
--- a/packages/cli-core/src/commands/init/frameworks/nuxt.ts
+++ b/packages/cli-core/src/commands/init/frameworks/nuxt.ts
@@ -9,6 +9,7 @@ import {
   headerHtmlBlock,
   htmlAuthComponentMarkup,
   indentBlock,
+  printModule,
   scaffoldAuthFiles,
   scaffoldConfigFile,
   scaffoldEnvVars,
@@ -46,7 +47,7 @@ function addNuxtModule(content: string): string {
 
     if (!defaultExport.modules) defaultExport.modules = [];
     if (Array.isArray(defaultExport.modules)) defaultExport.modules.push("@clerk/nuxt");
-    return mod.generate().code;
+    return printModule(mod, content);
   } catch {
     if (content.includes("modules:")) {
       return content.replace(/(modules:\s*\[)/, "$1\n    '@clerk/nuxt',");
diff --git a/packages/cli-core/src/commands/init/frameworks/react-router.test.ts b/packages/cli-core/src/commands/init/frameworks/react-router.test.ts
index 7d198f64c..bc6c18eab 100644
--- a/packages/cli-core/src/commands/init/frameworks/react-router.test.ts
+++ b/packages/cli-core/src/commands/init/frameworks/react-router.test.ts
@@ -420,6 +420,7 @@ export default {
   if (configAction?.type !== "modify") throw new Error("Expected config modify action");
 
   expect(configAction.content).toContain("v8_middleware: true");
+  expect(configAction.content.endsWith("\n")).toBe(true);
 });
 
 test("does not enable v8_middleware for React Router 8", async () => {
@@ -496,6 +497,7 @@ export default defineConfig({
   expect(viteAction.content).toContain("noExternal");
   expect(viteAction.content).toContain("@clerk/react-router");
   expect(viteAction.content.match(/ssr\s*:/g)?.length).toBe(1);
+  expect(viteAction.content.endsWith("\n")).toBe(true);
 });
 
 test("appends to an existing ssr.noExternal array for React Router 8", async () => {
diff --git a/packages/cli-core/src/commands/init/frameworks/react-router.ts b/packages/cli-core/src/commands/init/frameworks/react-router.ts
index 6242771b2..c2679cb49 100644
--- a/packages/cli-core/src/commands/init/frameworks/react-router.ts
+++ b/packages/cli-core/src/commands/init/frameworks/react-router.ts
@@ -10,6 +10,7 @@ import {
   jsxAuthPageContent,
   jsxExt,
   parseMajorVersion,
+  printModule,
   safeAddImport,
   scaffoldAuthFiles,
   scaffoldConfigFile,
@@ -215,7 +216,7 @@ function enableV8Middleware(content: string): string {
 
     if (!defaultExport.future) defaultExport.future = {};
     defaultExport.future.v8_middleware = true;
-    return mod.generate().code;
+    return printModule(mod, content);
   } catch {
     if (content.includes("future:")) {
       return content.replace(/(future:\s*\{)/, "$1\n    v8_middleware: true,");
@@ -415,7 +416,7 @@ function addClerkNoExternal(content: string): string {
     if (!config.ssr.noExternal.includes("@clerk/react-router")) {
       config.ssr.noExternal.push("@clerk/react-router");
     }
-    return mod.generate().code;
+    return printModule(mod, content);
   } catch {
     return content;
   }
diff --git a/packages/cli-core/src/commands/init/frameworks/transformations.test.ts b/packages/cli-core/src/commands/init/frameworks/transformations.test.ts
index 358200b9a..cc68e9d18 100644
--- a/packages/cli-core/src/commands/init/frameworks/transformations.test.ts
+++ b/packages/cli-core/src/commands/init/frameworks/transformations.test.ts
@@ -1,5 +1,53 @@
 import { test, expect, describe } from "bun:test";
-import { addSuspenseImport, insertAfterLastImport } from "./transformations.ts";
+import { parseModule } from "magicast";
+import {
+  addSuspenseImport,
+  insertAfterLastImport,
+  printModule,
+  safeAddImport,
+} from "./transformations.ts";
+
+describe("printModule", () => {
+  test.each([
+    ["LF", "\n"],
+    ["CRLF", "\r\n"],
+  ])("keeps the source's %s line endings, including the trailing one", (_name, eol) => {
+    const source = `export default {${eol}  a: 1,${eol}};${eol}`;
+    const mod = parseModule(source);
+    mod.exports.default.b = 2;
+
+    const result = printModule(mod, source);
+
+    expect(result).toBe(`export default {${eol}  a: 1,${eol}  b: 2,${eol}};${eol}`);
+  });
+
+  test("keeps CRLF line endings when the source ended without one", () => {
+    const source = `export default {\r\n  a: 1,\r\n};`;
+    const mod = parseModule(source);
+    mod.exports.default.b = 2;
+
+    expect(printModule(mod, source)).toBe(`export default {\r\n  a: 1,\r\n  b: 2,\r\n};`);
+  });
+
+  test("adds no line break when the source ended without one", () => {
+    const source = `export default {\n  a: 1,\n};`;
+    const mod = parseModule(source);
+    mod.exports.default.b = 2;
+
+    expect(printModule(mod, source).endsWith(";")).toBe(true);
+  });
+});
+
+describe("safeAddImport", () => {
+  test("keeps the trailing newline", () => {
+    const source = `import "./globals.css";\n\nexport default function RootLayout() {\n  return null;\n}\n`;
+
+    const result = safeAddImport(source, "@clerk/nextjs", "ClerkProvider");
+
+    expect(result).toContain('import { ClerkProvider } from "@clerk/nextjs";');
+    expect(result.endsWith("}\n")).toBe(true);
+  });
+});
 
 describe("insertAfterLastImport", () => {
   test("inserts after a single-line import", () => {
diff --git a/packages/cli-core/src/commands/init/frameworks/transformations.ts b/packages/cli-core/src/commands/init/frameworks/transformations.ts
index 27206effd..5afe60699 100644
--- a/packages/cli-core/src/commands/init/frameworks/transformations.ts
+++ b/packages/cli-core/src/commands/init/frameworks/transformations.ts
@@ -3,9 +3,21 @@
  * These functions take source code as input and return modified source code.
  * Used by framework scaffolders for import injection, provider wrapping, and indentation.
  */
-import { parseModule } from "magicast";
+import { parseModule, type ProxifiedModule } from "magicast";
 import { maskCommentsAndStrings } from "./source-scan.js";
 
+/**
+ * Print a magicast module in the line endings of the source it was parsed from, keeping
+ * its trailing line break. magicast's printer joins lines with the host's EOL and drops
+ * the final line break, which leaves "No newline at end of file" in the user's diff.
+ */
+export function printModule(mod: ProxifiedModule, source: string): string {
+  const lineTerminator = /\r?\n/.exec(source)?.[0] ?? "\n";
+  const code = mod.generate({ lineTerminator }).code;
+  const eol = /\r?\n$/.exec(source)?.[0];
+  return eol && !code.endsWith("\n") ? code + eol : code;
+}
+
 /** Check if file content already imports from a @clerk/ package. */
 export function hasClerkImport(content: string): boolean {
   return content.includes("@clerk/");
@@ -30,7 +42,10 @@ export function safeAddImport(content: string, source: string, imported: string)
     // spacing, and no printer option overrides that. Projects without a
     // formatter would keep `import {x}`, so re-space the one statement we
     // added — anchored on `from` so only an import statement can match.
-    return mod.generate().code.replace(`import {${imported}} from`, `import { ${imported} } from`);
+    return printModule(mod, content).replace(
+      `import {${imported}} from`,
+      `import { ${imported} } from`,
+    );
   } catch {
     return `import { ${imported} } from "${source}";\n${content}`;
   }