diff --git a/.changeset/init-keeps-line-endings.md b/.changeset/init-keeps-line-endings.md
new file mode 100644
index 0000000..d9d89a4
--- /dev/null
+++ b/.changeset/init-keeps-line-endings.md
@@ -0,0 +1,5 @@
+---
+"@paramour-js/next": patch
+---
+
+`paramour init` keeps the line endings of the files it edits. In a CRLF checkout (git `core.autocrlf=true`), it used to report "updated paramour section" for an unchanged `AGENTS.md`/`CLAUDE.md` section and leave the file with mixed CRLF and LF line endings. It also rewrote a CRLF `package.json` or `next.config` entirely in LF. It now recognizes its own section regardless of line endings, and writes each edit using the file's existing line ending. Wrapping `next.config` also no longer drops the file's final newline.
diff --git a/packages/next/src/emit.ts b/packages/next/src/emit.ts
index b78daac..ad85f66 100644
--- a/packages/next/src/emit.ts
+++ b/packages/next/src/emit.ts
@@ -15,6 +15,16 @@ export interface WriteIfChangedResult {
   written: boolean;
 }
 
+/**
+ * The line ending a user-owned file already uses. Init edits files the user
+ * owns (package.json, next.config, AGENTS.md), and writing LF text into a CRLF file
+ * leaves mixed endings, so those edits keep the file's own ending. Generated
+ * files are always written LF instead.
+ */
+export function lineEnding(text: string): "\n" | "\r\n" {
+  return text.includes("\r\n") ? "\r\n" : "\n";
+}
+
 /**
  * Content equality that ignores CRLF vs LF. A consumer repo with git
  * `core.autocrlf=true` checks the committed LF artifact out as CRLF; that
diff --git a/packages/next/src/init/agents-md.ts b/packages/next/src/init/agents-md.ts
index 77867dd..85d5ca3 100644
--- a/packages/next/src/init/agents-md.ts
+++ b/packages/next/src/init/agents-md.ts
@@ -1,6 +1,8 @@
 import { existsSync } from "node:fs";
 import { join } from "node:path";
 
+import { lineEnding, sameContent } from "../emit.js";
+
 export const AGENTS_MARKER_START = "<!-- paramour:start -->";
 export const AGENTS_MARKER_END = "<!-- paramour:end -->";
 
@@ -59,20 +61,21 @@ export function upsertAgentsSection(text: string): {
   status: "added" | "unchanged" | "unterminated" | "updated";
   text: string;
 } {
+  const eol = lineEnding(text);
+  const snippet = agentsSnippet().replaceAll("\n", eol);
   const start = text.indexOf(AGENTS_MARKER_START);
   if (start === -1) {
-    const base = text === "" || text.endsWith("\n") ? text : `${text}\n`;
-    const separator = base === "" ? "" : "\n";
+    const base = text === "" || text.endsWith("\n") ? text : `${text}${eol}`;
+    const separator = base === "" ? "" : eol;
     return {
       status: "added",
-      text: `${base}${separator}${agentsSnippet()}\n`,
+      text: `${base}${separator}${snippet}${eol}`,
     };
   }
   const end = text.indexOf(AGENTS_MARKER_END, start);
   if (end === -1) return { status: "unterminated", text };
   const current = text.slice(start, end + AGENTS_MARKER_END.length);
-  const snippet = agentsSnippet();
-  if (current === snippet) return { status: "unchanged", text };
+  if (sameContent(current, snippet)) return { status: "unchanged", text };
   return {
     status: "updated",
     text:
diff --git a/packages/next/src/init/scaffold.ts b/packages/next/src/init/scaffold.ts
index 885104d..fda9340 100644
--- a/packages/next/src/init/scaffold.ts
+++ b/packages/next/src/init/scaffold.ts
@@ -1,6 +1,7 @@
 import { existsSync, readFileSync } from "node:fs";
 import { join, relative } from "node:path";
 
+import { lineEnding } from "../emit.js";
 import { resolveRouteDirs } from "../scan.js";
 import { loadPackagedSkill } from "../skills/packaged.js";
 import { auditTarget, isOutdated } from "../skills/sync.js";
@@ -15,9 +16,9 @@ export interface SetupCheck {
 
 /**
  * Insert `"paramour": "paramour generate"` into a package.json's scripts,
- * preserving the file's own indentation and trailing-newline choice.
- * Throws on malformed JSON — a broken package.json is init's one hard
- * prerequisite failure.
+ * preserving the file's own indentation, line ending, and trailing-newline
+ * choice. Throws on malformed JSON — a broken package.json is init's one
+ * hard prerequisite failure.
  */
 export function addPackageScript(text: string): {
   changed: boolean;
@@ -41,8 +42,12 @@ export function addPackageScript(text: string): {
   if (scripts?.paramour !== undefined) return { changed: false, text };
   pkg.scripts = { ...scripts, paramour: "paramour generate" };
   const indent = /^([ \t]+)"/m.exec(text)?.[1] ?? "  ";
-  const trailing = text.endsWith("\n") ? "\n" : "";
-  return { changed: true, text: JSON.stringify(pkg, null, indent) + trailing };
+  const eol = lineEnding(text);
+  const trailing = text.endsWith("\n") ? eol : "";
+  return {
+    changed: true,
+    text: JSON.stringify(pkg, null, indent).replaceAll("\n", eol) + trailing,
+  };
 }
 
 /**
diff --git a/packages/next/src/init/wrap-next-config.ts b/packages/next/src/init/wrap-next-config.ts
index 72cb0de..648008d 100644
--- a/packages/next/src/init/wrap-next-config.ts
+++ b/packages/next/src/init/wrap-next-config.ts
@@ -1,6 +1,8 @@
 import { existsSync } from "node:fs";
 import { join } from "node:path";
 
+import { lineEnding } from "../emit.js";
+
 /**
  * The `paramour init` next.config codemod (magicast: recast printing +
  * babel-ts parsing, so TS/ESM configs transform format-preservingly).
@@ -179,7 +181,12 @@ export async function wrapNextConfigSource(
       local ?? "withTypedRoutes",
       current,
     );
-    return { code: generateCode(mod).code, status: "wrapped" };
+    // recast prints new nodes with LF and drops the final newline; keep the
+    // user's file as it was on both counts.
+    const eol = lineEnding(source);
+    let code = generateCode(mod).code.replaceAll("\r\n", "\n");
+    if (source.endsWith("\n") && !code.endsWith("\n")) code += "\n";
+    return { code: code.replaceAll("\n", eol), status: "wrapped" };
   } catch {
     return { snippet: manualSnippet(), status: "manual" };
   }
diff --git a/packages/next/test/init.test.ts b/packages/next/test/init.test.ts
index 301fdf1..a50d339 100644
--- a/packages/next/test/init.test.ts
+++ b/packages/next/test/init.test.ts
@@ -573,6 +573,59 @@ describe("paramour init", () => {
     expect(snapshotTree(root)).toEqual(before);
   });
 
+  it("treats a CRLF checkout of its own section as up to date", async () => {
+    // git core.autocrlf=true checks the committed LF file out as CRLF.
+    const checkedOut = `${AGENTS_MD}\n${agentsSnippet()}\n`.replaceAll(
+      "\n",
+      "\r\n",
+    );
+    const root = makeProject(["app/page.tsx"], {
+      "CLAUDE.md": checkedOut,
+      "package.json": PACKAGE_JSON,
+    });
+    const run = await init(["--no-wrap"]);
+    expect(run.out.join("\n")).toContain(
+      "• CLAUDE.md paramour section already up to date — skipped",
+    );
+    expect(readFileSync(join(root, "CLAUDE.md"), "utf8")).toBe(checkedOut);
+  });
+
+  it("keeps a CRLF instructions file CRLF when appending and updating", async () => {
+    const root = makeProject(["app/page.tsx"], {
+      "AGENTS.md": AGENTS_MD.replaceAll("\n", "\r\n"),
+      "package.json": PACKAGE_JSON,
+    });
+    await init(["--no-wrap"]);
+    const appended = readFileSync(join(root, "AGENTS.md"), "utf8");
+    expect(appended).toContain(AGENTS_MARKER_START);
+    expect(appended).not.toMatch(/(?<!\r)\n/);
+
+    writeFileSync(
+      join(root, "AGENTS.md"),
+      appended.replace("## paramour", "## paramour (edited)"),
+    );
+    const run = await init(["--no-wrap"]);
+    expect(run.out.join("\n")).toContain(
+      "✔ updated paramour section in AGENTS.md",
+    );
+    const updated = readFileSync(join(root, "AGENTS.md"), "utf8");
+    expect(updated).toBe(appended);
+  });
+
+  it("keeps a CRLF package.json CRLF when adding the script", async () => {
+    const root = makeProject(["app/page.tsx"], {
+      "package.json": PACKAGE_JSON.replaceAll("\n", "\r\n"),
+    });
+    const run = await init(["--no-wrap"]);
+    expect(run.out.join("\n")).toContain(
+      `✔ added "paramour" script to package.json`,
+    );
+    const text = readFileSync(join(root, "package.json"), "utf8");
+    expect(text).toContain('"paramour": "paramour generate"');
+    expect(text).not.toMatch(/(?<!\r)\n/);
+    expect(text.endsWith("}\r\n")).toBe(true);
+  });
+
   it("starts the section on its own line when the file lacks a trailing newline", async () => {
     const root = makeProject(["app/page.tsx"], {
       "AGENTS.md": "# Notes without newline",
diff --git a/packages/next/test/wrap-next-config.test.ts b/packages/next/test/wrap-next-config.test.ts
index 56172d5..e6f2cd6 100644
--- a/packages/next/test/wrap-next-config.test.ts
+++ b/packages/next/test/wrap-next-config.test.ts
@@ -30,6 +30,29 @@ describe("wrapNextConfigSource", () => {
     );
     // The untouched parts keep their original formatting (recast).
     expect(result.code).toContain("  reactStrictMode: true,");
+    expect(
+      result.code.endsWith("export default withTypedRoutes(nextConfig);\n"),
+    ).toBe(true);
+  });
+
+  it("keeps a CRLF config CRLF, including the added import", async () => {
+    const result = await wrapNextConfigSource(
+      IDENTIFIER_TS.replaceAll("\n", "\r\n"),
+    );
+    expect(result.status).toBe("wrapped");
+    if (result.status !== "wrapped") return;
+    expect(result.code).toContain(
+      "export default withTypedRoutes(nextConfig);",
+    );
+    expect(result.code).not.toMatch(/(?<!\r)\n/);
+    expect(result.code.endsWith(";\r\n")).toBe(true);
+  });
+
+  it("does not add a final newline the source did not have", async () => {
+    const result = await wrapNextConfigSource(IDENTIFIER_TS.trimEnd());
+    expect(result.status).toBe("wrapped");
+    if (result.status !== "wrapped") return;
+    expect(result.code.endsWith("withTypedRoutes(nextConfig);")).toBe(true);
   });
 
   it("wraps an object-literal default export", async () => {