diff --git a/.changeset/fix-example-monkey.md b/.changeset/fix-example-monkey.md
new file mode 100644
index 00000000..90771087
--- /dev/null
+++ b/.changeset/fix-example-monkey.md
@@ -0,0 +1,5 @@
+---
+'dotenv-diff': patch
+---
+
+fix: auto-generated `.env.example` no longer copies non-key lines, such as the body of a multi-line quoted value (e.g. a PEM private key)
diff --git a/docs/configuration_and_flags.md b/docs/configuration_and_flags.md
index e88cd36f..15e9a3a3 100644
--- a/docs/configuration_and_flags.md
+++ b/docs/configuration_and_flags.md
@@ -342,8 +342,8 @@ Usage in the configuration file:
 
 ### `--ci`
 
-Run in CI mode: non-interactive and read-only.
-Prevents all file creation and modification, including prompts for missing files.
+Run in CI mode: non-interactive.
+Disables prompts and never creates missing files. Files are only modified if you also pass [`--fix`](#--fix) explicitly.
 Always exits with an error if issues are found. Recommended for CI/CD pipelines.
 
 Example usage:
diff --git a/docs/index.md b/docs/index.md
index 3aabcdd7..29442fa5 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -31,7 +31,7 @@ npx dotenv-diff
 ```
 
 If no `.env` files are found, `dotenv-diff` will prompt you to create one (interactive mode only).
-Use `--yes` to auto-accept prompts, or `--ci` to disable prompts and run read-only.
+Use `--yes` to auto-accept prompts, or `--ci` to disable prompts and never create missing files.
 If you choose not to create a file, `dotenv-diff` will still scan your codebase for environment variable usage, but it will not compare results against an `.env` file.
 
 
diff --git a/packages/cli/src/cli/program.ts b/packages/cli/src/cli/program.ts
index 7cab3054..26ed8e55 100644
--- a/packages/cli/src/cli/program.ts
+++ b/packages/cli/src/cli/program.ts
@@ -124,7 +124,10 @@ export function createProgram() {
         '--baseline',
         'Set current codebase state as baseline for future comparisons',
       )
-      .option('--ci', 'Run non-interactively and never create files')
+      .option(
+        '--ci',
+        'Run non-interactively and never create missing files (--fix still applies)',
+      )
       .option('-y, --yes', 'Run non-interactively and answer Yes to prompts')
 
       // Output
diff --git a/packages/cli/src/commands/prompts/promptEnsureFiles.ts b/packages/cli/src/commands/prompts/promptEnsureFiles.ts
index bfb2aee0..b0933ac2 100644
--- a/packages/cli/src/commands/prompts/promptEnsureFiles.ts
+++ b/packages/cli/src/commands/prompts/promptEnsureFiles.ts
@@ -4,6 +4,7 @@ import { confirmYesNo } from './prompts.js';
 import { warnIfEnvNotIgnored } from '../../services/git.js';
 import { printPrompt } from '../../ui/compare/printPrompt.js';
 import { DEFAULT_ENV_FILE } from '../../config/constants.js';
+import { parseEnvLine, splitEnvLines } from '../../core/envLine.js';
 
 /**
  * Result of ensureFilesOrPrompt function
@@ -121,20 +122,59 @@ export async function promptEnsureFiles(
       return EXIT_WITHOUT_CREATING;
     }
 
-    const envContent = fs
-      .readFileSync(envPath, 'utf-8')
-      .split('\n')
-      .map((line) => {
-        const trimmed = line.trim();
-        if (!trimmed || trimmed.startsWith('#')) return trimmed;
-        const [key] = trimmed.split('=');
-        return `${key}=`;
-      })
-      .join('\n');
-
-    fs.writeFileSync(examplePath, envContent);
+    const exampleContent = toExampleContent(fs.readFileSync(envPath, 'utf-8'));
+
+    fs.writeFileSync(examplePath, exampleContent);
     printPrompt.exampleCreated(examplePath, envPath);
   }
 
   return { didCreate: true, shouldExit: false, exitCode: 0 };
 }
+
+/**
+ * Builds .env.example content from .env content. Keeps comments and blank
+ * lines, strips every value, and drops anything that is not a `KEY=value`
+ * line, such as the body of a multi-line quoted value (fx a PEM key), so no
+ * secret material ends up in a file meant to be committed.
+ * @param envContent - Raw content of the .env file
+ * @returns Content for the .env.example file
+ */
+export function toExampleContent(envContent: string): string {
+  const lines: string[] = [];
+  let openQuote: string | null = null;
+
+  for (const line of splitEnvLines(envContent)) {
+    const trimmed = line.trim();
+
+    // Inside a multi-line quoted value: skip until the closing quote
+    if (openQuote) {
+      if (trimmed.includes(openQuote)) openQuote = null;
+      continue;
+    }
+
+    if (!trimmed || trimmed.startsWith('#')) {
+      lines.push(trimmed);
+      continue;
+    }
+
+    const parsed = parseEnvLine(line);
+    if (!parsed) continue;
+
+    lines.push(`${parsed.key}=`);
+    openQuote = unclosedQuote(parsed.value);
+  }
+
+  return lines.join('\n');
+}
+
+/**
+ * Returns the quote character a value opens without closing on the same line.
+ * fx: `"-----BEGIN KEY-----` → `"`, `"closed"` → null, `plain` → null
+ * @param value - The value part of a dotenv line
+ * @returns The unclosed quote character, or null
+ */
+function unclosedQuote(value: string): string | null {
+  const quote = value[0];
+  if (quote !== '"' && quote !== "'" && quote !== '`') return null;
+  return value.indexOf(quote, 1) === -1 ? quote : null;
+}
diff --git a/packages/cli/test/unit/commands/prompts/promptEnsureFiles.test.ts b/packages/cli/test/unit/commands/prompts/promptEnsureFiles.test.ts
index 9c68b885..45d21a73 100644
--- a/packages/cli/test/unit/commands/prompts/promptEnsureFiles.test.ts
+++ b/packages/cli/test/unit/commands/prompts/promptEnsureFiles.test.ts
@@ -2,7 +2,10 @@ import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import fs from 'fs';
 import path from 'path';
 import os from 'os';
-import { promptEnsureFiles } from '../../../../src/commands/prompts/promptEnsureFiles.js';
+import {
+  promptEnsureFiles,
+  toExampleContent,
+} from '../../../../src/commands/prompts/promptEnsureFiles.js';
 
 // ---- mocks ----
 vi.mock('../../../../src/commands/prompts/prompts.js', () => ({
@@ -41,7 +44,7 @@ describe('promptEnsureFiles', () => {
   it('includes Do you want to create message in the confirmYesNo prompt text', async () => {
     fs.writeFileSync(path.join(cwd, '.env.example'), 'FOO=bar');
 
-    (confirmYesNo as any).mockResolvedValue(true);
+    vi.mocked(confirmYesNo).mockResolvedValue(true);
 
     await promptEnsureFiles({
       cwd,
@@ -78,7 +81,7 @@ describe('promptEnsureFiles', () => {
   it('does not create .env when user declines', async () => {
     fs.writeFileSync(path.join(cwd, '.env.example'), 'FOO=bar');
 
-    (confirmYesNo as any).mockResolvedValue(false);
+    vi.mocked(confirmYesNo).mockResolvedValue(false);
 
     const result = await promptEnsureFiles({
       cwd,
@@ -96,7 +99,7 @@ describe('promptEnsureFiles', () => {
   it('creates .env when user confirms via interactive prompt', async () => {
     fs.writeFileSync(path.join(cwd, '.env.example'), 'FOO=bar');
 
-    (confirmYesNo as any).mockResolvedValue(true);
+    vi.mocked(confirmYesNo).mockResolvedValue(true);
 
     const result = await promptEnsureFiles({
       cwd,
@@ -136,7 +139,7 @@ describe('promptEnsureFiles', () => {
   it('skips creating .env.example when user declines', async () => {
     fs.writeFileSync(path.join(cwd, '.env'), 'FOO=bar');
 
-    (confirmYesNo as any).mockResolvedValue(false);
+    vi.mocked(confirmYesNo).mockResolvedValue(false);
 
     const result = await promptEnsureFiles({
       cwd,
@@ -277,3 +280,46 @@ BAZ=123
     expect(result.shouldExit).toBe(false);
   });
 });
+
+describe('toExampleContent', () => {
+  it('keeps comments and blank lines and strips values', () => {
+    expect(toExampleContent('# db\nFOO=bar\n\nBAZ=123\n')).toBe(
+      '# db\nFOO=\n\nBAZ=\n',
+    );
+  });
+
+  it('never copies the body of a multi-line quoted value', () => {
+    const env = [
+      'API=1',
+      'PRIVATE_KEY="-----BEGIN RSA PRIVATE KEY-----',
+      'MIIEsecretBODYline',
+      'abcd==',
+      '-----END RSA PRIVATE KEY-----"',
+      'AFTER=2',
+    ].join('\n');
+
+    expect(toExampleContent(env)).toBe('API=\nPRIVATE_KEY=\nAFTER=');
+  });
+
+  it('handles single quotes and a trailing comment after the closing quote', () => {
+    const env = "CERT='line1\nline2' # cert\nNEXT=1";
+
+    expect(toExampleContent(env)).toBe('CERT=\nNEXT=');
+  });
+
+  it('treats a value that opens and closes its quote on one line as complete', () => {
+    expect(toExampleContent('A="x"\nB=\'y\' # c\nC=`z`\nD=1')).toBe(
+      'A=\nB=\nC=\nD=',
+    );
+  });
+
+  it('drops lines that are not KEY=value', () => {
+    expect(toExampleContent('FOO=1\njust some text\n=nokey\nBAR=2')).toBe(
+      'FOO=\nBAR=',
+    );
+  });
+
+  it('handles CRLF line endings and a BOM', () => {
+    expect(toExampleContent('\uFEFFFOO=1\r\nBAR=2\r\n')).toBe('FOO=\nBAR=\n');
+  });
+});