diff --git a/src/config/config.ts b/src/config/config.ts
index baa0179a01..4761b7b215 100644
--- a/src/config/config.ts
+++ b/src/config/config.ts
@@ -13,6 +13,7 @@ export * from "./types.js";
 export {
   validateConfigObject,
   validateConfigObjectRaw,
+  validateConfigObjectRawWithPlugins,
   validateConfigObjectWithPlugins,
 } from "./validation.js";
 export { OpenClawSchema } from "./zod-schema.js";
diff --git a/src/config/io.ts b/src/config/io.ts
index 0164a2231a..19b1f02e73 100644
--- a/src/config/io.ts
+++ b/src/config/io.ts
@@ -3,6 +3,7 @@ import crypto from "node:crypto";
 import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
+import { isDeepStrictEqual } from "node:util";
 import type { OpenClawConfig, ConfigFileSnapshot, LegacyConfigIssue } from "./types.js";
 import { loadDotEnv } from "../infra/dotenv.js";
 import { resolveRequiredHomeDir } from "../infra/home-dir.js";
@@ -28,10 +29,14 @@ import { MissingEnvVarError, resolveConfigEnvVars } from "./env-substitution.js"
 import { collectConfigEnvVars } from "./env-vars.js";
 import { ConfigIncludeError, resolveConfigIncludes } from "./includes.js";
 import { findLegacyConfigIssues } from "./legacy.js";
+import { applyMergePatch } from "./merge-patch.js";
 import { normalizeConfigPaths } from "./normalize-paths.js";
 import { resolveConfigPath, resolveDefaultConfigCandidates, resolveStateDir } from "./paths.js";
 import { applyConfigOverrides } from "./runtime-overrides.js";
-import { validateConfigObjectWithPlugins } from "./validation.js";
+import {
+  validateConfigObjectRawWithPlugins,
+  validateConfigObjectWithPlugins,
+} from "./validation.js";
 import { compareOpenClawVersions } from "./version.js";
 
 // Re-export for backwards compatibility
@@ -92,6 +97,49 @@ function coerceConfig(value: unknown): OpenClawConfig {
   return value as OpenClawConfig;
 }
 
+function isPlainObject(value: unknown): value is Record<string, unknown> {
+  return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+
+function cloneUnknown<T>(value: T): T {
+  return structuredClone(value);
+}
+
+function createMergePatch(base: unknown, target: unknown): unknown {
+  if (!isPlainObject(base) || !isPlainObject(target)) {
+    return cloneUnknown(target);
+  }
+
+  const patch: Record<string, unknown> = {};
+  const keys = new Set([...Object.keys(base), ...Object.keys(target)]);
+  for (const key of keys) {
+    const hasBase = key in base;
+    const hasTarget = key in target;
+    if (!hasTarget) {
+      patch[key] = null;
+      continue;
+    }
+    const targetValue = target[key];
+    if (!hasBase) {
+      patch[key] = cloneUnknown(targetValue);
+      continue;
+    }
+    const baseValue = base[key];
+    if (isPlainObject(baseValue) && isPlainObject(targetValue)) {
+      const childPatch = createMergePatch(baseValue, targetValue);
+      if (isPlainObject(childPatch) && Object.keys(childPatch).length === 0) {
+        continue;
+      }
+      patch[key] = childPatch;
+      continue;
+    }
+    if (!isDeepStrictEqual(baseValue, targetValue)) {
+      patch[key] = cloneUnknown(targetValue);
+    }
+  }
+  return patch;
+}
+
 async function rotateConfigBackups(configPath: string, ioFs: typeof fs.promises): Promise<void> {
   if (CONFIG_BACKUP_COUNT <= 1) {
     return;
@@ -502,7 +550,14 @@ export function createConfigIO(overrides: ConfigIoDeps = {}) {
 
   async function writeConfigFile(cfg: OpenClawConfig) {
     clearConfigCache();
-    const validated = validateConfigObjectWithPlugins(cfg);
+    let persistCandidate: unknown = cfg;
+    const snapshot = await readConfigFileSnapshot();
+    if (snapshot.valid && snapshot.exists) {
+      const patch = createMergePatch(snapshot.config, cfg);
+      persistCandidate = applyMergePatch(snapshot.resolved, patch);
+    }
+
+    const validated = validateConfigObjectRawWithPlugins(persistCandidate);
     if (!validated.ok) {
       const issue = validated.issues[0];
       const pathLabel = issue?.path ? issue.path : "<root>";
@@ -518,7 +573,9 @@ export function createConfigIO(overrides: ConfigIoDeps = {}) {
     await deps.fs.promises.mkdir(dir, { recursive: true, mode: 0o700 });
     // Do NOT apply runtime defaults when writing — user config should only contain
     // explicitly set values. Runtime defaults are applied when loading (issue #6070).
-    const json = JSON.stringify(stampConfigVersion(cfg), null, 2).trimEnd().concat("\n");
+    const json = JSON.stringify(stampConfigVersion(validated.config), null, 2)
+      .trimEnd()
+      .concat("\n");
 
     const tmp = path.join(
       dir,
diff --git a/src/config/io.write-config.test.ts b/src/config/io.write-config.test.ts
new file mode 100644
index 0000000000..cff5cd245e
--- /dev/null
+++ b/src/config/io.write-config.test.ts
@@ -0,0 +1,47 @@
+import fs from "node:fs/promises";
+import path from "node:path";
+import { describe, expect, it } from "vitest";
+import { createConfigIO } from "./io.js";
+import { withTempHome } from "./test-helpers.js";
+
+describe("config io write", () => {
+  it("persists caller changes onto resolved config without leaking runtime defaults", async () => {
+    await withTempHome(async (home) => {
+      const configPath = path.join(home, ".openclaw", "openclaw.json");
+      await fs.mkdir(path.dirname(configPath), { recursive: true });
+      await fs.writeFile(
+        configPath,
+        JSON.stringify({ gateway: { port: 18789 } }, null, 2),
+        "utf-8",
+      );
+
+      const io = createConfigIO({
+        env: {} as NodeJS.ProcessEnv,
+        homedir: () => home,
+      });
+
+      const snapshot = await io.readConfigFileSnapshot();
+      expect(snapshot.valid).toBe(true);
+
+      const next = structuredClone(snapshot.config);
+      next.gateway = {
+        ...next.gateway,
+        auth: { mode: "token" },
+      };
+
+      await io.writeConfigFile(next);
+
+      const persisted = JSON.parse(await fs.readFile(configPath, "utf-8")) as Record<
+        string,
+        unknown
+      >;
+      expect(persisted.gateway).toEqual({
+        port: 18789,
+        auth: { mode: "token" },
+      });
+      expect(persisted).not.toHaveProperty("agents.defaults");
+      expect(persisted).not.toHaveProperty("messages.ackReaction");
+      expect(persisted).not.toHaveProperty("sessions.persistence");
+    });
+  });
+});
diff --git a/src/config/validation.ts b/src/config/validation.ts
index 7cb702985e..9f01ad1b24 100644
--- a/src/config/validation.ts
+++ b/src/config/validation.ts
@@ -156,7 +156,38 @@ export function validateConfigObjectWithPlugins(raw: unknown):
       issues: ConfigValidationIssue[];
       warnings: ConfigValidationIssue[];
     } {
-  const base = validateConfigObject(raw);
+  return validateConfigObjectWithPluginsBase(raw, { applyDefaults: true });
+}
+
+export function validateConfigObjectRawWithPlugins(raw: unknown):
+  | {
+      ok: true;
+      config: OpenClawConfig;
+      warnings: ConfigValidationIssue[];
+    }
+  | {
+      ok: false;
+      issues: ConfigValidationIssue[];
+      warnings: ConfigValidationIssue[];
+    } {
+  return validateConfigObjectWithPluginsBase(raw, { applyDefaults: false });
+}
+
+function validateConfigObjectWithPluginsBase(
+  raw: unknown,
+  opts: { applyDefaults: boolean },
+):
+  | {
+      ok: true;
+      config: OpenClawConfig;
+      warnings: ConfigValidationIssue[];
+    }
+  | {
+      ok: false;
+      issues: ConfigValidationIssue[];
+      warnings: ConfigValidationIssue[];
+    } {
+  const base = opts.applyDefaults ? validateConfigObject(raw) : validateConfigObjectRaw(raw);
   if (!base.ok) {
     return { ok: false, issues: base.issues, warnings: [] };
   }