diff --git a/src/targets/codex.ts b/src/targets/codex.ts
index f38a4dd..9e8ba8b 100644
--- a/src/targets/codex.ts
+++ b/src/targets/codex.ts
@@ -1,5 +1,5 @@
 import path from "path"
-import { copyDir, ensureDir, writeText } from "../utils/files"
+import { backupFile, copyDir, ensureDir, writeText } from "../utils/files"
 import type { CodexBundle } from "../types/codex"
 import type { ClaudeMcpServer } from "../types/claude"
 
@@ -30,7 +30,12 @@ export async function writeCodexBundle(outputRoot: string, bundle: CodexBundle):
 
   const config = renderCodexConfig(bundle.mcpServers)
   if (config) {
-    await writeText(path.join(codexRoot, "config.toml"), config)
+    const configPath = path.join(codexRoot, "config.toml")
+    const backupPath = await backupFile(configPath)
+    if (backupPath) {
+      console.log(`Backed up existing config to ${backupPath}`)
+    }
+    await writeText(configPath, config)
   }
 }
 
diff --git a/src/targets/opencode.ts b/src/targets/opencode.ts
index 09f372a..24e8faf 100644
--- a/src/targets/opencode.ts
+++ b/src/targets/opencode.ts
@@ -1,10 +1,15 @@
 import path from "path"
-import { copyDir, ensureDir, writeJson, writeText } from "../utils/files"
+import { backupFile, copyDir, ensureDir, writeJson, writeText } from "../utils/files"
 import type { OpenCodeBundle } from "../types/opencode"
 
 export async function writeOpenCodeBundle(outputRoot: string, bundle: OpenCodeBundle): Promise<void> {
   const paths = resolveOpenCodePaths(outputRoot)
   await ensureDir(paths.root)
+
+  const backupPath = await backupFile(paths.configPath)
+  if (backupPath) {
+    console.log(`Backed up existing config to ${backupPath}`)
+  }
   await writeJson(paths.configPath, bundle.config)
 
   const agentsDir = paths.agentsDir
diff --git a/src/utils/files.ts b/src/utils/files.ts
index 5fd1453..9994d0c 100644
--- a/src/utils/files.ts
+++ b/src/utils/files.ts
@@ -1,6 +1,19 @@
 import { promises as fs } from "fs"
 import path from "path"
 
+export async function backupFile(filePath: string): Promise<string | null> {
+  if (!(await pathExists(filePath))) return null
+
+  try {
+    const timestamp = new Date().toISOString().replace(/[:.]/g, "-")
+    const backupPath = `${filePath}.bak.${timestamp}`
+    await fs.copyFile(filePath, backupPath)
+    return backupPath
+  } catch {
+    return null
+  }
+}
+
 export async function pathExists(filePath: string): Promise<boolean> {
   try {
     await fs.access(filePath)
diff --git a/tests/codex-writer.test.ts b/tests/codex-writer.test.ts
index ad2f03a..3aeb42e 100644
--- a/tests/codex-writer.test.ts
+++ b/tests/codex-writer.test.ts
@@ -73,4 +73,36 @@ describe("writeCodexBundle", () => {
     expect(await exists(path.join(codexRoot, "prompts", "command-one.md"))).toBe(true)
     expect(await exists(path.join(codexRoot, "skills", "skill-one", "SKILL.md"))).toBe(true)
   })
+
+  test("backs up existing config.toml before overwriting", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "codex-backup-"))
+    const codexRoot = path.join(tempRoot, ".codex")
+    const configPath = path.join(codexRoot, "config.toml")
+
+    // Create existing config
+    await fs.mkdir(codexRoot, { recursive: true })
+    const originalContent = "# My original config\n[custom]\nkey = \"value\"\n"
+    await fs.writeFile(configPath, originalContent)
+
+    const bundle: CodexBundle = {
+      prompts: [],
+      skillDirs: [],
+      generatedSkills: [],
+      mcpServers: { test: { command: "echo" } },
+    }
+
+    await writeCodexBundle(codexRoot, bundle)
+
+    // New config should be written
+    const newConfig = await fs.readFile(configPath, "utf8")
+    expect(newConfig).toContain("[mcp_servers.test]")
+
+    // Backup should exist with original content
+    const files = await fs.readdir(codexRoot)
+    const backupFileName = files.find((f) => f.startsWith("config.toml.bak."))
+    expect(backupFileName).toBeDefined()
+
+    const backupContent = await fs.readFile(path.join(codexRoot, backupFileName!), "utf8")
+    expect(backupContent).toBe(originalContent)
+  })
 })
diff --git a/tests/opencode-writer.test.ts b/tests/opencode-writer.test.ts
index c481520..0bafcc0 100644
--- a/tests/opencode-writer.test.ts
+++ b/tests/opencode-writer.test.ts
@@ -84,4 +84,36 @@ describe("writeOpenCodeBundle", () => {
     expect(await exists(path.join(outputRoot, "skills", "skill-one", "SKILL.md"))).toBe(true)
     expect(await exists(path.join(outputRoot, ".opencode"))).toBe(false)
   })
+
+  test("backs up existing opencode.json before overwriting", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "opencode-backup-"))
+    const outputRoot = path.join(tempRoot, ".opencode")
+    const configPath = path.join(outputRoot, "opencode.json")
+
+    // Create existing config
+    await fs.mkdir(outputRoot, { recursive: true })
+    const originalConfig = { $schema: "https://opencode.ai/config.json", custom: "value" }
+    await fs.writeFile(configPath, JSON.stringify(originalConfig, null, 2))
+
+    const bundle: OpenCodeBundle = {
+      config: { $schema: "https://opencode.ai/config.json", new: "config" },
+      agents: [],
+      plugins: [],
+      skillDirs: [],
+    }
+
+    await writeOpenCodeBundle(outputRoot, bundle)
+
+    // New config should be written
+    const newConfig = JSON.parse(await fs.readFile(configPath, "utf8"))
+    expect(newConfig.new).toBe("config")
+
+    // Backup should exist with original content
+    const files = await fs.readdir(outputRoot)
+    const backupFileName = files.find((f) => f.startsWith("opencode.json.bak."))
+    expect(backupFileName).toBeDefined()
+
+    const backupContent = JSON.parse(await fs.readFile(path.join(outputRoot, backupFileName!), "utf8"))
+    expect(backupContent.custom).toBe("value")
+  })
 })