diff --git a/package.json b/package.json
index a78bc4b..e55b295 100644
--- a/package.json
+++ b/package.json
@@ -27,7 +27,7 @@
     "dev": "rslib build --watch",
     "lint": "biome check .",
     "lint:write": "biome check . --write",
-    "prepare": "simple-git-hooks && npm run build",
+    "prepare": "simple-git-hooks && pnpm run build",
     "test": "rstest run",
     "bump": "npx bumpp"
   },
diff --git a/src/index.ts b/src/index.ts
index fe0c749..e44f43f 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -204,7 +204,7 @@ export async function create({
 
   const cwd = process.cwd();
   const pkgInfo = pkgFromUserAgent(process.env.npm_config_user_agent);
-  const pkgManager = pkgInfo ? pkgInfo.name : 'npm';
+  const packageManager = pkgInfo ? pkgInfo.name : 'npm';
 
   // No version provided, read from package.json
   if (!version) {
@@ -264,12 +264,14 @@ export async function create({
     to: distFolder,
     version,
     skipFiles,
+    packageManager,
   });
   copyFolder({
     from: srcFolder,
     to: distFolder,
     version,
     packageName,
+    packageManager,
     skipFiles,
   });
 
@@ -294,6 +296,7 @@ export async function create({
         to: distFolder,
         version,
         skipFiles,
+        packageManager,
         isMergePackageJson: true,
       });
 
@@ -307,6 +310,7 @@ export async function create({
       to: distFolder,
       version,
       skipFiles,
+      packageManager,
       isMergePackageJson: true,
     });
 
@@ -324,7 +328,10 @@ export async function create({
   if (agentsFiles.length > 0) {
     const mergedAgents = mergeAgentsFiles(agentsFiles);
     const agentsPath = path.join(distFolder, 'AGENTS.md');
-    fs.writeFileSync(agentsPath, `${mergedAgents}\n`);
+    fs.writeFileSync(
+      agentsPath,
+      `${replacePlaceholder(mergedAgents, packageManager)}\n`,
+    );
   }
 
   const nextSteps = noteInformation
@@ -332,8 +339,8 @@ export async function create({
     : [
         `1. ${color.cyan(`cd ${targetDir}`)}`,
         `2. ${color.cyan('git init')} ${color.dim('(optional)')}`,
-        `3. ${color.cyan(`${pkgManager} install`)}`,
-        `4. ${color.cyan(`${pkgManager} run dev`)}`,
+        `3. ${color.cyan(`${packageManager} install`)}`,
+        `4. ${color.cyan(`${packageManager} run dev`)}`,
       ];
 
   if (nextSteps.length) {
@@ -382,6 +389,12 @@ export function mergePackageJson(targetPackage: string, extraPackage: string) {
   fs.writeFileSync(targetPackage, `${JSON.stringify(mergedJson, null, 2)}\n`);
 }
 
+const isMarkdown = (file: string) =>
+  file.endsWith('.md') || file.endsWith('.mdx');
+
+const replacePlaceholder = (content: string, packageManager: string) =>
+  content.replace(/{{ packageManager }}/g, packageManager);
+
 /**
  * Copy files from one folder to another.
  * @param from Source folder
@@ -396,6 +409,7 @@ export function copyFolder({
   to,
   version,
   packageName,
+  packageManager,
   isMergePackageJson,
   skipFiles = [],
 }: {
@@ -403,6 +417,7 @@ export function copyFolder({
   to: string;
   version?: string | Record<string, string>;
   packageName?: string;
+  packageManager: string;
   isMergePackageJson?: boolean;
   skipFiles?: string[];
 }) {
@@ -430,6 +445,7 @@ export function copyFolder({
       copyFolder({
         from: srcFile,
         to: distFile,
+        packageManager,
         version,
         skipFiles,
       });
@@ -444,6 +460,11 @@ export function copyFolder({
       updatePackageJson(distFile, version, packageName);
     } else {
       fs.copyFileSync(srcFile, distFile);
+
+      if (isMarkdown(distFile)) {
+        const content = fs.readFileSync(distFile, 'utf-8');
+        fs.writeFileSync(distFile, replacePlaceholder(content, packageManager));
+      }
     }
   }
 }
diff --git a/template-biome/AGENTS.md b/template-biome/AGENTS.md
index c26c433..a5be109 100644
--- a/template-biome/AGENTS.md
+++ b/template-biome/AGENTS.md
@@ -2,5 +2,5 @@
 
 ### Biome
 
-- Run `npm run lint` to lint your code
-- Run `npm run format` to format your code
+- Run `{{ packageManager }} run lint` to lint your code
+- Run `{{ packageManager }} run format` to format your code
diff --git a/template-eslint/AGENTS.md b/template-eslint/AGENTS.md
index 2226fc4..209e9bc 100644
--- a/template-eslint/AGENTS.md
+++ b/template-eslint/AGENTS.md
@@ -2,4 +2,4 @@
 
 ### ESLint
 
-- Run `npm run lint` to lint your code
+- Run `{{ packageManager }} run lint` to lint your code
diff --git a/template-prettier/AGENTS.md b/template-prettier/AGENTS.md
index 7b57953..ebc03f4 100644
--- a/template-prettier/AGENTS.md
+++ b/template-prettier/AGENTS.md
@@ -2,4 +2,4 @@
 
 ### Prettier
 
-- Run `npm run format` to format your code
+- Run `{{ packageManager }} run format` to format your code
diff --git a/test/agents.test.ts b/test/agents.test.ts
index 66da09b..b1c0b04 100644
--- a/test/agents.test.ts
+++ b/test/agents.test.ts
@@ -62,7 +62,7 @@ test('should generate AGENTS.md with no tools selected', async () => {
 
     ### Rstest
 
-    - Run \`npm run test\` to test your code
+    - Run \`pnpm run test\` to test your code
 
     ## Template Info
 
@@ -117,12 +117,12 @@ test('should generate AGENTS.md with single tool selected', async () => {
 
     ### Rstest
 
-    - Run \`npm run test\` to test your code
+    - Run \`pnpm run test\` to test your code
 
     ### Biome
 
-    - Run \`npm run lint\` to lint your code
-    - Run \`npm run format\` to format your code
+    - Run \`pnpm run lint\` to lint your code
+    - Run \`pnpm run format\` to format your code
 
     ## Template Info
 
@@ -180,11 +180,11 @@ test('should generate AGENTS.md with eslint tool and template mapping', async ()
 
     ### Rstest
 
-    - Run \`npm run test\` to test your code
+    - Run \`pnpm run test\` to test your code
 
     ### ESLint
 
-    - Run \`npm run lint\` to lint your code
+    - Run \`pnpm run lint\` to lint your code
 
     ## Template Info
 
@@ -230,7 +230,7 @@ test('should merge top-level sections from AGENTS.md files', async () => {
 
     ### Rstest
 
-    - Run \`npm run test\` to test your code
+    - Run \`pnpm run test\` to test your code
 
     ## Template Info
 
diff --git a/test/fixtures/agents-md/template-vanilla/AGENTS.md b/test/fixtures/agents-md/template-vanilla/AGENTS.md
index 7c49a5f..ba83971 100644
--- a/test/fixtures/agents-md/template-vanilla/AGENTS.md
+++ b/test/fixtures/agents-md/template-vanilla/AGENTS.md
@@ -9,4 +9,4 @@
 
 ### Rstest
 
-- Run `npm run test` to test your code
+- Run `{{ packageManager }} run test` to test your code