diff --git a/CHANGELOG.md b/CHANGELOG.md
index dae426d06f2..101c5f74b84 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -598,6 +598,7 @@ Docs: https://docs.openclaw.ai
 
 ### Fixes
 
+- Config: serialize and retry semantic config mutations centrally, so concurrent commands can rebase safe changes instead of clobbering or hand-rolling command-local retry loops.
 - Models/auth: keep `agents.defaults.model` when `openclaw models auth login` runs without `--set-default`, so provider onboarding patches add models without silently switching the primary. Fixes #78162. (#78241) Thanks @neeravmakwana.
 - Control UI/chat: localize the remaining chat welcome, composer, run-control, session/model/thinking selector, and zh-CN Skills labels through the Control UI i18n pipeline so non-English browser locales no longer see those chat controls in English. Fixes #79937. Thanks @BunsDev.
 - Control UI: surface browser-blocked WebSocket security failures with wss:// and loopback dashboard guidance instead of leaving the connection on a dead security error. Thanks @BunsDev.
diff --git a/src/cli/plugins-install-record-commit.ts b/src/cli/plugins-install-record-commit.ts
index 4cda3f3c36c..468017eb63d 100644
--- a/src/cli/plugins-install-record-commit.ts
+++ b/src/cli/plugins-install-record-commit.ts
@@ -1,5 +1,14 @@
 import { isDeepStrictEqual } from "node:util";
-import { replaceConfigFile } from "../config/config.js";
+import {
+  replaceConfigFile,
+  resolveConfigWriteAfterWrite,
+  transformConfigFileWithRetry,
+  type ConfigMutationCommit,
+  type ConfigMutationResult,
+  type ConfigMutationContext,
+  type ConfigTransformResult,
+  type TransformConfigFileWithRetryParams,
+} from "../config/config.js";
 import type { ConfigWriteOptions } from "../config/io.js";
 import type { OpenClawConfig } from "../config/types.openclaw.js";
 import type { PluginInstallRecord } from "../config/types.plugins.js";
@@ -21,6 +30,19 @@ function mergeUnsetPaths(
 type ConfigCommit = (config: OpenClawConfig, writeOptions?: ConfigWriteOptions) => Promise<void>;
 const PLUGIN_SOURCE_CHANGED_RESTART_REASON = "plugin source changed";
 
+function mergeAfterWrite(
+  writeOptions: ConfigWriteOptions | undefined,
+  afterWrite: ConfigWriteOptions["afterWrite"],
+): ConfigWriteOptions | undefined {
+  if (afterWrite === undefined) {
+    return writeOptions;
+  }
+  return {
+    ...writeOptions,
+    afterWrite,
+  };
+}
+
 async function commitPluginInstallRecordsWithWriter(params: {
   previousInstallRecords?: Record<string, PluginInstallRecord>;
   nextInstallRecords: Record<string, PluginInstallRecord>;
@@ -141,3 +163,53 @@ export async function commitConfigWithPendingPluginInstalls(params: {
     },
   });
 }
+
+export async function transformConfigWithPendingPluginInstalls<T = void>(
+  params: Omit<TransformConfigFileWithRetryParams<T>, "commit">,
+): Promise<ConfigMutationResult<T>> {
+  const commit: ConfigMutationCommit = async ({ nextConfig, snapshot, baseHash, writeOptions }) => {
+    const requestedAfterWrite = params.afterWrite ?? params.writeOptions?.afterWrite;
+    const committed = await commitConfigWriteWithPendingPluginInstalls({
+      nextConfig,
+      ...(writeOptions ? { writeOptions: mergeAfterWrite(writeOptions, params.afterWrite) } : {}),
+      commit: async (config, commitWriteOptions) => {
+        await replaceConfigFile({
+          nextConfig: config,
+          snapshot,
+          writeOptions: commitWriteOptions ?? {},
+          ...(baseHash !== undefined ? { baseHash } : {}),
+        });
+      },
+    });
+    const afterWrite = resolveConfigWriteAfterWrite(
+      requestedAfterWrite ??
+        (committed.movedInstallRecords
+          ? { mode: "restart", reason: PLUGIN_SOURCE_CHANGED_RESTART_REASON }
+          : undefined),
+    );
+    return {
+      config: committed.config,
+      afterWrite,
+    };
+  };
+
+  return await transformConfigFileWithRetry<T>({
+    ...params,
+    commit,
+  });
+}
+
+export async function mutateConfigWithPendingPluginInstalls<T = void>(
+  params: Omit<TransformConfigFileWithRetryParams<T>, "commit" | "transform"> & {
+    mutate: (draft: OpenClawConfig, context: ConfigMutationContext) => Promise<T | void> | T | void;
+  },
+): Promise<ConfigMutationResult<T>> {
+  return await transformConfigWithPendingPluginInstalls<T>({
+    ...params,
+    transform: async (currentConfig, context): Promise<ConfigTransformResult<T>> => {
+      const draft = structuredClone(currentConfig) as OpenClawConfig;
+      const result = (await params.mutate(draft, context)) as T | undefined;
+      return { nextConfig: draft, result };
+    },
+  });
+}
diff --git a/src/commands/agents.add.test.ts b/src/commands/agents.add.test.ts
index 76d9b1513a8..fbdda748921 100644
--- a/src/commands/agents.add.test.ts
+++ b/src/commands/agents.add.test.ts
@@ -13,6 +13,45 @@ const writeConfigFileMock = vi.hoisted(() => vi.fn().mockResolvedValue(undefined
 const replaceConfigFileMock = vi.hoisted(() =>
   vi.fn(async (params: { nextConfig: unknown }) => await writeConfigFileMock(params.nextConfig)),
 );
+const transformConfigWithPendingPluginInstallsMock = vi.hoisted(() =>
+  vi.fn(
+    async (params: {
+      transform: (
+        config: Record<string, unknown>,
+        context: {
+          snapshot: Record<string, unknown>;
+          previousHash: string | null;
+          attempt: number;
+        },
+      ) =>
+        | Promise<{ nextConfig: unknown; result?: unknown }>
+        | { nextConfig: unknown; result?: unknown };
+    }) => {
+      const snapshot = (await readConfigFileSnapshotMock()) as {
+        path?: string;
+        hash?: string;
+        config?: Record<string, unknown>;
+        sourceConfig?: Record<string, unknown>;
+      };
+      const transformed = await params.transform(snapshot.sourceConfig ?? snapshot.config ?? {}, {
+        snapshot,
+        previousHash: snapshot.hash ?? null,
+        attempt: 0,
+      });
+      await writeConfigFileMock(transformed.nextConfig);
+      return {
+        path: snapshot.path ?? "/tmp/openclaw.json",
+        previousHash: snapshot.hash ?? null,
+        snapshot,
+        nextConfig: transformed.nextConfig,
+        result: transformed.result,
+        attempts: 1,
+        afterWrite: { mode: "auto" },
+        followUp: { mode: "auto", requiresRestart: false },
+      };
+    },
+  ),
+);
 
 const wizardMocks = vi.hoisted(() => ({
   createClackPrompter: vi.fn(),
@@ -25,6 +64,13 @@ vi.mock("../config/config.js", async () => ({
   replaceConfigFile: replaceConfigFileMock,
 }));
 
+vi.mock("../cli/plugins-install-record-commit.js", async () => ({
+  ...(await vi.importActual<typeof import("../cli/plugins-install-record-commit.js")>(
+    "../cli/plugins-install-record-commit.js",
+  )),
+  transformConfigWithPendingPluginInstalls: transformConfigWithPendingPluginInstallsMock,
+}));
+
 vi.mock("../wizard/clack-prompter.js", () => ({
   createClackPrompter: wizardMocks.createClackPrompter,
 }));
@@ -44,6 +90,7 @@ describe("agents add command", () => {
     readConfigFileSnapshotMock.mockClear();
     writeConfigFileMock.mockClear();
     replaceConfigFileMock.mockClear();
+    transformConfigWithPendingPluginInstallsMock.mockClear();
     wizardMocks.createClackPrompter.mockClear();
     runtime.log.mockClear();
     runtime.error.mockClear();
@@ -227,4 +274,98 @@ describe("agents add command", () => {
       }),
     ).toBe('OAuth profiles stay shared from "main" unless this agent signs in separately.');
   });
+
+  describe("non-interactive config mutation", () => {
+    it("rebases agent creation on the latest config snapshot", async () => {
+      readConfigFileSnapshotMock
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-1",
+          config: { agents: { list: [] } },
+          sourceConfig: { agents: { list: [] } },
+        })
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-2",
+          config: { agents: { list: [{ id: "other-agent" }] } },
+          sourceConfig: { agents: { list: [{ id: "other-agent" }] } },
+        });
+
+      await agentsAddCommand({ name: "Work", workspace: "/tmp/work" }, runtime, {
+        hasFlags: true,
+      });
+
+      expect(transformConfigWithPendingPluginInstallsMock).toHaveBeenCalledOnce();
+      expect(writeConfigFileMock).toHaveBeenCalledWith(
+        expect.objectContaining({
+          agents: {
+            list: [
+              { id: "other-agent" },
+              expect.objectContaining({ id: "work", workspace: "/tmp/work" }),
+            ],
+          },
+        }),
+      );
+      expect(runtime.exit).not.toHaveBeenCalled();
+      expect(runtime.error).not.toHaveBeenCalled();
+    });
+
+    it("fails instead of overwriting when the same agent appears before commit", async () => {
+      readConfigFileSnapshotMock
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-1",
+          config: { agents: { list: [] } },
+          sourceConfig: { agents: { list: [] } },
+        })
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-2",
+          config: { agents: { list: [{ id: "work", workspace: "/tmp/other" }] } },
+          sourceConfig: { agents: { list: [{ id: "work", workspace: "/tmp/other" }] } },
+        });
+
+      await agentsAddCommand({ name: "Work", workspace: "/tmp/work" }, runtime, {
+        hasFlags: true,
+      });
+
+      expect(writeConfigFileMock).not.toHaveBeenCalled();
+      expect(runtime.error).toHaveBeenCalledWith('Agent "work" already exists.');
+      expect(runtime.exit).toHaveBeenCalledWith(1);
+    });
+
+    it("reports binding conflicts from the committed mutation", async () => {
+      readConfigFileSnapshotMock
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-1",
+          config: { agents: { list: [] } },
+          sourceConfig: { agents: { list: [] } },
+        })
+        .mockResolvedValueOnce({
+          ...baseConfigSnapshot,
+          hash: "hash-2",
+          config: {
+            agents: { list: [{ id: "other-agent" }] },
+            bindings: [{ type: "route", agentId: "other-agent", match: { channel: "telegram" } }],
+          },
+          sourceConfig: {
+            agents: { list: [{ id: "other-agent" }] },
+            bindings: [{ type: "route", agentId: "other-agent", match: { channel: "telegram" } }],
+          },
+        });
+
+      await agentsAddCommand(
+        { name: "Work", workspace: "/tmp/work", bind: ["telegram"], json: true },
+        runtime,
+        { hasFlags: true },
+      );
+
+      const payload = JSON.parse(String(runtime.log.mock.calls.at(-1)?.[0])) as {
+        bindings: { added: string[]; conflicts: string[] };
+      };
+      expect(payload.bindings.added).toEqual([]);
+      expect(payload.bindings.conflicts).toEqual(["telegram (agent=other-agent)"]);
+    });
+  });
 });
diff --git a/src/commands/agents.commands.add.ts b/src/commands/agents.commands.add.ts
index e3f562d1e6f..9010301bc43 100644
--- a/src/commands/agents.commands.add.ts
+++ b/src/commands/agents.commands.add.ts
@@ -15,7 +15,10 @@ import {
   loadPersistedAuthProfileStore,
 } from "../agents/auth-profiles/persisted.js";
 import { formatCliCommand } from "../cli/command-format.js";
-import { commitConfigWithPendingPluginInstalls } from "../cli/plugins-install-record-commit.js";
+import {
+  commitConfigWithPendingPluginInstalls,
+  transformConfigWithPendingPluginInstalls,
+} from "../cli/plugins-install-record-commit.js";
 import { logConfigUpdated } from "../config/logging.js";
 import { pathExists } from "../infra/fs-safe.js";
 import { saveJsonFile } from "../infra/json-file.js";
@@ -53,6 +56,24 @@ type AgentsAddOptions = {
   json?: boolean;
 };
 
+type AgentBindingResult = ReturnType<typeof applyAgentBindings>;
+
+type AgentsAddMutationResult = {
+  agentDir: string;
+  bindingResult: AgentBindingResult;
+};
+
+class AgentsAddMutationError extends Error {
+  constructor(message: string) {
+    super(message);
+    this.name = "AgentsAddMutationError";
+  }
+}
+
+function emptyBindingResult(config: Parameters<typeof applyAgentBindings>[0]): AgentBindingResult {
+  return { config, added: [], updated: [], skipped: [], conflicts: [] };
+}
+
 async function copyPortableAuthProfiles(params: {
   destAuthPath: string;
   sourceAgentDir: string;
@@ -147,44 +168,64 @@ export async function agentsAddCommand(
     }
 
     const workspaceDir = resolveUserPath(workspaceFlag);
-    const agentDir = opts.agentDir?.trim()
+    const explicitAgentDir = opts.agentDir?.trim()
       ? resolveUserPath(opts.agentDir.trim())
-      : resolveAgentDir(cfg, agentId);
+      : undefined;
     const model = opts.model?.trim();
-    const nextConfig = applyAgentConfig(cfg, {
-      agentId,
-      name: nameInput,
-      workspace: workspaceDir,
-      agentDir,
-      ...(model ? { model } : {}),
-    });
 
-    const bindingParse = parseBindingSpecs({
-      agentId,
-      specs: opts.bind,
-      config: nextConfig,
-    });
-    if (bindingParse.errors.length > 0) {
-      runtime.error(bindingParse.errors.join("\n"));
-      runtime.exit(1);
-      return;
+    let committed;
+    try {
+      committed = await transformConfigWithPendingPluginInstalls<AgentsAddMutationResult>({
+        transform: (latestConfig) => {
+          if (findAgentEntryIndex(listAgentEntries(latestConfig), agentId) >= 0) {
+            throw new AgentsAddMutationError(`Agent "${agentId}" already exists.`);
+          }
+          const agentDir = explicitAgentDir ?? resolveAgentDir(latestConfig, agentId);
+          const nextConfig = applyAgentConfig(latestConfig, {
+            agentId,
+            name: nameInput,
+            workspace: workspaceDir,
+            agentDir,
+            ...(model ? { model } : {}),
+          });
+          const bindingParse = parseBindingSpecs({
+            agentId,
+            specs: opts.bind,
+            config: nextConfig,
+          });
+          if (bindingParse.errors.length > 0) {
+            throw new AgentsAddMutationError(bindingParse.errors.join("\n"));
+          }
+          const bindingResult =
+            bindingParse.bindings.length > 0
+              ? applyAgentBindings(nextConfig, bindingParse.bindings)
+              : emptyBindingResult(nextConfig);
+          return {
+            nextConfig: bindingResult.config,
+            result: { agentDir, bindingResult },
+          };
+        },
+      });
+    } catch (err) {
+      if (err instanceof AgentsAddMutationError) {
+        runtime.error(err.message);
+        runtime.exit(1);
+        return;
+      }
+      throw err;
     }
-    const bindingResult =
-      bindingParse.bindings.length > 0
-        ? applyAgentBindings(nextConfig, bindingParse.bindings)
-        : { config: nextConfig, added: [], updated: [], skipped: [], conflicts: [] };
-
-    await commitConfigWithPendingPluginInstalls({
-      nextConfig: bindingResult.config,
-      ...(baseHash !== undefined ? { baseHash } : {}),
-    });
+    const mutationResult = committed.result;
+    if (!mutationResult) {
+      throw new Error("Agent config mutation did not return a result.");
+    }
+    const { agentDir, bindingResult } = mutationResult;
     if (!opts.json) {
       logConfigUpdated(runtime);
     }
     const quietRuntime = opts.json ? createQuietRuntime(runtime) : runtime;
     await ensureWorkspaceAndSessions(workspaceDir, quietRuntime, {
-      skipBootstrap: Boolean(bindingResult.config.agents?.defaults?.skipBootstrap),
-      skipOptionalBootstrapFiles: bindingResult.config.agents?.defaults?.skipOptionalBootstrapFiles,
+      skipBootstrap: Boolean(committed.nextConfig.agents?.defaults?.skipBootstrap),
+      skipOptionalBootstrapFiles: committed.nextConfig.agents?.defaults?.skipOptionalBootstrapFiles,
       agentId,
     });
 
diff --git a/src/config/config.ts b/src/config/config.ts
index 9ce646c9b02..c67e3021688 100644
--- a/src/config/config.ts
+++ b/src/config/config.ts
@@ -43,7 +43,25 @@ export type {
   ConfigWriteNotification,
   ReadConfigFileSnapshotWithPluginMetadataResult,
 } from "./io.js";
-export { ConfigMutationConflictError, mutateConfigFile, replaceConfigFile } from "./mutate.js";
+export {
+  ConfigMutationConflictError,
+  mutateConfigFile,
+  mutateConfigFileWithRetry,
+  replaceConfigFile,
+  transformConfigFile,
+  transformConfigFileWithRetry,
+} from "./mutate.js";
+export type {
+  ConfigMutationCommit,
+  ConfigMutationCommitParams,
+  ConfigMutationCommitResult,
+  ConfigMutationContext,
+  ConfigMutationIO,
+  ConfigMutationResult,
+  ConfigTransformResult,
+  TransformConfigFileParams,
+  TransformConfigFileWithRetryParams,
+} from "./mutate.js";
 export {
   assertConfigWriteAllowedInCurrentMode,
   NixModeConfigMutationError,
diff --git a/src/config/io.ts b/src/config/io.ts
index 25761a0b7ad..9722ee47631 100644
--- a/src/config/io.ts
+++ b/src/config/io.ts
@@ -2428,6 +2428,7 @@ export async function writeConfigFile(
     nextCfg = coerceConfig(applyMergePatch(runtimeConfigSourceSnapshot!, runtimePatch));
   }
   const writeResult = await io.writeConfigFile(nextCfg, {
+    baseSnapshot: options.baseSnapshot,
     envSnapshotForRestore: resolveWriteEnvSnapshotForPath({
       actualConfigPath: io.configPath,
       expectedConfigPath: options.expectedConfigPath,
@@ -2438,6 +2439,7 @@ export async function writeConfigFile(
     explicitSetValueSource: options.explicitSetPaths
       ? (options.explicitSetValueSource ?? cfg)
       : undefined,
+    afterWrite: options.afterWrite,
     allowDestructiveWrite: options.allowDestructiveWrite,
     allowConfigSizeDrop: options.allowConfigSizeDrop,
     skipRuntimeSnapshotRefresh: options.skipRuntimeSnapshotRefresh,
diff --git a/src/config/mutate.test.ts b/src/config/mutate.test.ts
index 33ae28e235f..64d392a0180 100644
--- a/src/config/mutate.test.ts
+++ b/src/config/mutate.test.ts
@@ -2,7 +2,12 @@ import fs from "node:fs/promises";
 import path from "node:path";
 import { afterAll, beforeAll, beforeEach, describe, expect, it, vi } from "vitest";
 import { createSuiteTempRootTracker } from "../test-helpers/temp-dir.js";
-import { ConfigMutationConflictError, mutateConfigFile, replaceConfigFile } from "./mutate.js";
+import {
+  ConfigMutationConflictError,
+  mutateConfigFile,
+  replaceConfigFile,
+  transformConfigFileWithRetry,
+} from "./mutate.js";
 import { registerRuntimeConfigWriteListener, resetConfigRuntimeState } from "./runtime-snapshot.js";
 import type { ConfigFileSnapshot, OpenClawConfig } from "./types.js";
 
@@ -11,8 +16,16 @@ const ioMocks = vi.hoisted(() => ({
   resolveConfigSnapshotHash: vi.fn(),
   writeConfigFile: vi.fn(),
 }));
+const validationMocks = vi.hoisted(() => ({
+  validateConfigObjectWithPlugins: vi.fn((config: OpenClawConfig) => ({
+    ok: true,
+    config,
+    warnings: [],
+  })),
+}));
 
 vi.mock("./io.js", () => ioMocks);
+vi.mock("./validation.js", () => validationMocks);
 
 function createSnapshot(params: {
   hash: string;
@@ -61,6 +74,13 @@ describe("config mutate helpers", () => {
   beforeEach(() => {
     vi.clearAllMocks();
     resetConfigRuntimeState();
+    validationMocks.validateConfigObjectWithPlugins.mockImplementation(
+      (config: OpenClawConfig) => ({
+        ok: true,
+        config,
+        warnings: [],
+      }),
+    );
     ioMocks.resolveConfigSnapshotHash.mockImplementation(
       (snapshot: { hash?: string }) => snapshot.hash ?? null,
     );
@@ -103,7 +123,125 @@ describe("config mutate helpers", () => {
           auth: { mode: "token" },
         },
       },
-      { expectedConfigPath: snapshot.path, afterWrite: { mode: "auto" } },
+      { baseSnapshot: snapshot, expectedConfigPath: snapshot.path, afterWrite: { mode: "auto" } },
+    );
+  });
+
+  it("retries transform mutations on stale config conflicts", async () => {
+    const initial = createSnapshot({
+      hash: "hash-1",
+      sourceConfig: { agents: { list: [] } },
+    });
+    const fresh = createSnapshot({
+      hash: "hash-2",
+      sourceConfig: { agents: { list: [{ id: "other-agent" }] } },
+    });
+    ioMocks.readConfigFileSnapshotForWrite
+      .mockResolvedValueOnce({
+        snapshot: initial,
+        writeOptions: { expectedConfigPath: initial.path },
+      })
+      .mockResolvedValueOnce({
+        snapshot: fresh,
+        writeOptions: { expectedConfigPath: fresh.path },
+      });
+    ioMocks.writeConfigFile
+      .mockRejectedValueOnce(new ConfigMutationConflictError("stale", { currentHash: "hash-2" }))
+      .mockResolvedValueOnce(undefined);
+
+    const result = await transformConfigFileWithRetry({
+      io: ioMocks,
+      transform(config, context) {
+        return {
+          nextConfig: {
+            ...config,
+            agents: {
+              list: [...(config.agents?.list ?? []), { id: "work" }],
+            },
+          },
+          result: context.attempt,
+        };
+      },
+    });
+
+    expect(result.attempts).toBe(2);
+    expect(result.result).toBe(1);
+    expect(ioMocks.writeConfigFile).toHaveBeenCalledTimes(2);
+    expect(ioMocks.writeConfigFile).toHaveBeenNthCalledWith(
+      2,
+      {
+        agents: {
+          list: [{ id: "other-agent" }, { id: "work" }],
+        },
+      },
+      { baseSnapshot: fresh, expectedConfigPath: fresh.path, afterWrite: { mode: "auto" } },
+    );
+  });
+
+  it("serializes same-process transform mutations before reading snapshots", async () => {
+    const initial = createSnapshot({
+      hash: "hash-1",
+      sourceConfig: { agents: { list: [] } },
+    });
+    const fresh = createSnapshot({
+      hash: "hash-2",
+      sourceConfig: { agents: { list: [{ id: "first" }] } },
+    });
+    ioMocks.readConfigFileSnapshotForWrite
+      .mockResolvedValueOnce({
+        snapshot: initial,
+        writeOptions: { expectedConfigPath: initial.path },
+      })
+      .mockResolvedValueOnce({
+        snapshot: fresh,
+        writeOptions: { expectedConfigPath: fresh.path },
+      });
+    ioMocks.writeConfigFile.mockResolvedValue(undefined);
+
+    let releaseFirstTransform!: () => void;
+    let markFirstTransformStarted!: () => void;
+    const firstTransformStarted = new Promise<void>((resolve) => {
+      markFirstTransformStarted = resolve;
+    });
+    const first = transformConfigFileWithRetry({
+      transform: async (config) => {
+        markFirstTransformStarted();
+        await new Promise<void>((release) => {
+          releaseFirstTransform = release;
+        });
+        return {
+          nextConfig: {
+            ...config,
+            agents: { list: [{ id: "first" }] },
+          },
+        };
+      },
+    });
+    await firstTransformStarted;
+    const second = transformConfigFileWithRetry({
+      transform: (config) => ({
+        nextConfig: {
+          ...config,
+          agents: {
+            list: [...(config.agents?.list ?? []), { id: "second" }],
+          },
+        },
+      }),
+    });
+    await Promise.resolve();
+    await Promise.resolve();
+    expect(ioMocks.readConfigFileSnapshotForWrite).toHaveBeenCalledTimes(1);
+
+    releaseFirstTransform();
+    await Promise.all([first, second]);
+    expect(ioMocks.writeConfigFile).toHaveBeenNthCalledWith(
+      2,
+      {
+        agents: {
+          list: [{ id: "first" }, { id: "second" }],
+        },
+      },
+      { baseSnapshot: fresh, expectedConfigPath: fresh.path, afterWrite: { mode: "auto" } },
     );
   });
 
diff --git a/src/config/mutate.ts b/src/config/mutate.ts
index 3e6110b7775..cba2223ee4b 100644
--- a/src/config/mutate.ts
+++ b/src/config/mutate.ts
@@ -1,7 +1,9 @@
+import { AsyncLocalStorage } from "node:async_hooks";
 import fs from "node:fs/promises";
 import path from "node:path";
 import { isDeepStrictEqual } from "node:util";
 import { formatErrorMessage } from "../infra/errors.js";
+import { withFileLock } from "../infra/file-lock.js";
 import { replaceFileAtomic } from "../infra/replace-file.js";
 import { isPathInside } from "../security/scan-paths.js";
 import { isRecord } from "../utils.js";
@@ -16,6 +18,7 @@ import {
 } from "./io.js";
 import { applyUnsetPathsForWrite, resolveManagedUnsetPathsForWrite } from "./io.write-prepare.js";
 import { assertConfigWriteAllowedInCurrentMode } from "./nix-mode-write-guard.js";
+import { resolveConfigPath } from "./paths.js";
 import {
   createRuntimeConfigWriteNotification,
   finalizeRuntimeSnapshotWrite,
@@ -33,6 +36,21 @@ import { validateConfigObjectWithPlugins } from "./validation.js";
 
 export type ConfigMutationBase = "runtime" | "source";
 
+const CONFIG_MUTATION_LOCK_OPTIONS = {
+  retries: {
+    retries: 80,
+    factor: 1.2,
+    minTimeout: 25,
+    maxTimeout: 250,
+    randomize: true,
+  },
+  stale: 30_000,
+} as const;
+
+const DEFAULT_CONFIG_MUTATION_RETRY_ATTEMPTS = 5;
+const activeConfigMutationLocks = new AsyncLocalStorage<Set<string>>();
+const configMutationQueueTails = new Map<string, Promise<void>>();
+
 export class ConfigMutationConflictError extends Error {
   readonly currentHash: string | null;
 
@@ -52,11 +70,62 @@ export type ConfigReplaceResult = {
   followUp: ConfigWriteFollowUp;
 };
 
-type ConfigMutationIO = {
+export type ConfigMutationIO = {
   readConfigFileSnapshotForWrite: typeof readConfigFileSnapshotForWrite;
   writeConfigFile: (cfg: OpenClawConfig, options?: ConfigWriteOptions) => Promise<unknown>;
 };
 
+export type ConfigMutationContext = {
+  snapshot: ConfigFileSnapshot;
+  previousHash: string | null;
+  attempt: number;
+};
+
+export type ConfigTransformResult<T> = {
+  nextConfig: OpenClawConfig;
+  result?: T;
+};
+
+export type ConfigMutationCommitParams = {
+  nextConfig: OpenClawConfig;
+  snapshot: ConfigFileSnapshot;
+  baseHash?: string;
+  writeOptions?: ConfigWriteOptions;
+  afterWrite: ConfigWriteAfterWrite;
+  io?: ConfigMutationIO;
+};
+
+export type ConfigMutationCommitResult = {
+  config: OpenClawConfig;
+  afterWrite?: ConfigWriteAfterWrite;
+};
+
+export type ConfigMutationCommit = (
+  params: ConfigMutationCommitParams,
+) => Promise<ConfigMutationCommitResult>;
+
+export type TransformConfigFileParams<T> = {
+  base?: ConfigMutationBase;
+  baseHash?: string;
+  afterWrite?: ConfigWriteOptions["afterWrite"];
+  writeOptions?: ConfigWriteOptions;
+  io?: ConfigMutationIO;
+  commit?: ConfigMutationCommit;
+  transform: (
+    currentConfig: OpenClawConfig,
+    context: ConfigMutationContext,
+  ) => Promise<ConfigTransformResult<T>> | ConfigTransformResult<T>;
+};
+
+export type TransformConfigFileWithRetryParams<T> = TransformConfigFileParams<T> & {
+  maxAttempts?: number;
+};
+
+export type ConfigMutationResult<T> = ConfigReplaceResult & {
+  result: T | undefined;
+  attempts: number;
+};
+
 function assertBaseHashMatches(snapshot: ConfigFileSnapshot, expectedHash?: string): string | null {
   const currentHash = resolveConfigSnapshotHash(snapshot) ?? null;
   if (expectedHash !== undefined && expectedHash !== currentHash) {
@@ -67,6 +136,49 @@ function assertBaseHashMatches(snapshot: ConfigFileSnapshot, expectedHash?: stri
   return currentHash;
 }
 
+async function withConfigMutationLock<T>(
+  params: { io?: ConfigMutationIO; lockPath?: string },
+  fn: () => Promise<T>,
+): Promise<T> {
+  if (params.io) {
+    return await fn();
+  }
+  const configPath = path.resolve(params.lockPath ?? resolveConfigPath());
+  const activeLocks = activeConfigMutationLocks.getStore();
+  if (activeLocks?.has(configPath)) {
+    return await fn();
+  }
+  assertConfigWriteAllowedInCurrentMode({ configPath });
+  await fs.mkdir(path.dirname(configPath), { recursive: true, mode: 0o700 });
+
+  const previousTail = configMutationQueueTails.get(configPath) ?? Promise.resolve();
+  let releaseQueueSlot!: () => void;
+  const currentRun = new Promise<void>((resolve) => {
+    releaseQueueSlot = resolve;
+  });
+  const currentTail = previousTail.catch(() => undefined).then(() => currentRun);
+  configMutationQueueTails.set(configPath, currentTail);
+
+  await previousTail.catch(() => undefined);
+  try {
+    const nextActiveLocks = new Set(activeLocks ?? []);
+    nextActiveLocks.add(configPath);
+    return await activeConfigMutationLocks.run(
+      nextActiveLocks,
+      async () => await withFileLock(configPath, CONFIG_MUTATION_LOCK_OPTIONS, fn),
+    );
+  } finally {
+    releaseQueueSlot();
+    if (configMutationQueueTails.get(configPath) === currentTail) {
+      configMutationQueueTails.delete(configPath);
+    }
+  }
+}
+
+function markActiveConfigMutationPath(configPath: string): void {
+  activeConfigMutationLocks.getStore()?.add(path.resolve(configPath));
+}
+
 function getChangedTopLevelKeys(base: unknown, next: unknown): string[] {
   if (!isRecord(base) || !isRecord(next)) {
     return isDeepStrictEqual(base, next) ? [] : ["<root>"];
@@ -223,6 +335,20 @@ export async function replaceConfigFile(params: {
   afterWrite?: ConfigWriteOptions["afterWrite"];
   writeOptions?: ConfigWriteOptions;
   io?: ConfigMutationIO;
+}): Promise<ConfigReplaceResult> {
+  return await withConfigMutationLock(
+    { io: params.io, lockPath: params.snapshot?.path },
+    async () => await replaceConfigFileUnlocked(params),
+  );
+}
+
+async function replaceConfigFileUnlocked(params: {
+  nextConfig: OpenClawConfig;
+  baseHash?: string;
+  snapshot?: ConfigFileSnapshot;
+  afterWrite?: ConfigWriteOptions["afterWrite"];
+  writeOptions?: ConfigWriteOptions;
+  io?: ConfigMutationIO;
 }): Promise<ConfigReplaceResult> {
   const prepared =
     params.snapshot && params.writeOptions
@@ -230,6 +356,7 @@ export async function replaceConfigFile(params: {
       : await (params.io?.readConfigFileSnapshotForWrite ?? readConfigFileSnapshotForWrite)();
   const { snapshot, writeOptions } = prepared;
   assertConfigWriteAllowedInCurrentMode({ configPath: snapshot.path });
+  markActiveConfigMutationPath(snapshot.path);
   const previousHash = assertBaseHashMatches(snapshot, params.baseHash);
   const afterWrite = resolveConfigWriteAfterWrite(
     params.afterWrite ?? params.writeOptions?.afterWrite,
@@ -259,52 +386,138 @@ export async function replaceConfigFile(params: {
   };
 }
 
+async function commitPreparedConfigMutation(
+  params: ConfigMutationCommitParams,
+): Promise<ConfigMutationCommitResult> {
+  const result = await replaceConfigFileUnlocked({
+    nextConfig: params.nextConfig,
+    snapshot: params.snapshot,
+    baseHash: params.baseHash,
+    writeOptions: {
+      ...params.writeOptions,
+      afterWrite: params.afterWrite,
+    },
+    io: params.io,
+  });
+  return {
+    config: result.nextConfig,
+    afterWrite: result.afterWrite,
+  };
+}
+
+async function transformConfigFileAttempt<T>(
+  params: TransformConfigFileParams<T>,
+  attempt: number,
+): Promise<ConfigMutationResult<T>> {
+  const { snapshot, writeOptions } = await (
+    params.io?.readConfigFileSnapshotForWrite ?? readConfigFileSnapshotForWrite
+  )();
+  assertConfigWriteAllowedInCurrentMode({ configPath: snapshot.path });
+  markActiveConfigMutationPath(snapshot.path);
+  const previousHash = assertBaseHashMatches(snapshot, params.baseHash);
+  const baseConfig = params.base === "runtime" ? snapshot.runtimeConfig : snapshot.sourceConfig;
+  const afterWrite = resolveConfigWriteAfterWrite(
+    params.afterWrite ?? params.writeOptions?.afterWrite,
+  );
+  const mergedWriteOptions = {
+    ...writeOptions,
+    ...params.writeOptions,
+  };
+  const transformed = await params.transform(baseConfig, { snapshot, previousHash, attempt });
+  const committed = await (params.commit ?? commitPreparedConfigMutation)({
+    nextConfig: transformed.nextConfig,
+    snapshot,
+    ...(previousHash !== null ? { baseHash: previousHash } : {}),
+    writeOptions: mergedWriteOptions,
+    afterWrite,
+    io: params.io,
+  });
+  const committedAfterWrite = committed.afterWrite ?? afterWrite;
+  return {
+    path: snapshot.path,
+    previousHash,
+    snapshot,
+    nextConfig: committed.config,
+    result: transformed.result,
+    attempts: attempt + 1,
+    afterWrite: committedAfterWrite,
+    followUp: resolveConfigWriteFollowUp(committedAfterWrite),
+  };
+}
+
+export async function transformConfigFile<T = void>(
+  params: TransformConfigFileParams<T>,
+): Promise<ConfigMutationResult<T>> {
+  return await withConfigMutationLock(
+    { io: params.io },
+    async () => await transformConfigFileAttempt(params, 0),
+  );
+}
+
+export async function transformConfigFileWithRetry<T = void>(
+  params: TransformConfigFileWithRetryParams<T>,
+): Promise<ConfigMutationResult<T>> {
+  const maxAttempts = params.maxAttempts ?? DEFAULT_CONFIG_MUTATION_RETRY_ATTEMPTS;
+  if (!Number.isInteger(maxAttempts) || maxAttempts < 1) {
+    throw new Error("Config mutation maxAttempts must be a positive integer.");
+  }
+  return await withConfigMutationLock({ io: params.io }, async () => {
+    for (let attempt = 0; attempt < maxAttempts; attempt += 1) {
+      try {
+        return await transformConfigFileAttempt(params, attempt);
+      } catch (err) {
+        if (err instanceof ConfigMutationConflictError && attempt < maxAttempts - 1) {
+          continue;
+        }
+        throw err;
+      }
+    }
+    throw new Error("Config mutation retry loop exhausted unexpectedly.");
+  });
+}
+
 export async function mutateConfigFile<T = void>(params: {
   base?: ConfigMutationBase;
   baseHash?: string;
   afterWrite?: ConfigWriteOptions["afterWrite"];
   writeOptions?: ConfigWriteOptions;
   io?: ConfigMutationIO;
-  mutate: (
-    draft: OpenClawConfig,
-    context: { snapshot: ConfigFileSnapshot; previousHash: string | null },
-  ) => Promise<T | void> | T | void;
-}): Promise<ConfigReplaceResult & { result: T | undefined }> {
-  const { snapshot, writeOptions } = await (
-    params.io?.readConfigFileSnapshotForWrite ?? readConfigFileSnapshotForWrite
-  )();
-  assertConfigWriteAllowedInCurrentMode({ configPath: snapshot.path });
-  const previousHash = assertBaseHashMatches(snapshot, params.baseHash);
-  const baseConfig = params.base === "runtime" ? snapshot.runtimeConfig : snapshot.sourceConfig;
-  const draft = structuredClone(baseConfig) as OpenClawConfig;
-  const result = (await params.mutate(draft, { snapshot, previousHash })) as T | undefined;
-  const afterWrite = resolveConfigWriteAfterWrite(
-    params.afterWrite ?? params.writeOptions?.afterWrite,
-  );
-  const wroteInclude = await tryWriteSingleTopLevelIncludeMutation({
-    snapshot,
-    nextConfig: draft,
-    afterWrite,
-    writeOptions: {
-      ...writeOptions,
-      ...params.writeOptions,
-    },
+  mutate: (draft: OpenClawConfig, context: ConfigMutationContext) => Promise<T | void> | T | void;
+}): Promise<ConfigMutationResult<T>> {
+  return await transformConfigFile<T>({
+    base: params.base,
+    baseHash: params.baseHash,
+    afterWrite: params.afterWrite,
+    writeOptions: params.writeOptions,
     io: params.io,
+    transform: async (currentConfig, context) => {
+      const draft = structuredClone(currentConfig) as OpenClawConfig;
+      const result = (await params.mutate(draft, context)) as T | undefined;
+      return { nextConfig: draft, result };
+    },
+  });
+}
+
+export async function mutateConfigFileWithRetry<T = void>(params: {
+  base?: ConfigMutationBase;
+  baseHash?: string;
+  maxAttempts?: number;
+  afterWrite?: ConfigWriteOptions["afterWrite"];
+  writeOptions?: ConfigWriteOptions;
+  io?: ConfigMutationIO;
+  mutate: (draft: OpenClawConfig, context: ConfigMutationContext) => Promise<T | void> | T | void;
+}): Promise<ConfigMutationResult<T>> {
+  return await transformConfigFileWithRetry<T>({
+    base: params.base,
+    baseHash: params.baseHash,
+    maxAttempts: params.maxAttempts,
+    afterWrite: params.afterWrite,
+    writeOptions: params.writeOptions,
+    io: params.io,
+    transform: async (currentConfig, context) => {
+      const draft = structuredClone(currentConfig) as OpenClawConfig;
+      const result = (await params.mutate(draft, context)) as T | undefined;
+      return { nextConfig: draft, result };
+    },
   });
-  if (!wroteInclude) {
-    await (params.io?.writeConfigFile ?? writeConfigFile)(draft, {
-      ...writeOptions,
-      ...params.writeOptions,
-      afterWrite,
-    });
-  }
-  return {
-    path: snapshot.path,
-    previousHash,
-    snapshot,
-    nextConfig: draft,
-    result,
-    afterWrite,
-    followUp: resolveConfigWriteFollowUp(afterWrite),
-  };
 }