diff --git a/libs/deepagents/src/agent.ts b/libs/deepagents/src/agent.ts
index a864ae6c3..00c6b3e33 100644
--- a/libs/deepagents/src/agent.ts
+++ b/libs/deepagents/src/agent.ts
@@ -26,6 +26,7 @@ import {
 import { StateBackend } from "./backends/index.js";
 import { InteropZodObject } from "@langchain/core/utils/types";
 import { CompiledSubAgent } from "./middleware/subagents.js";
+import { mergeMiddleware } from "./middleware/utils.js";
 import type {
   CreateDeepAgentParams,
   DeepAgent,
@@ -201,10 +202,10 @@ export function createDeepAgent<
 
     return {
       ...subagent,
-      middleware: [
-        subagentSkillsMiddleware,
-        ...(subagent.middleware || []),
-      ] as readonly AgentMiddleware[],
+      middleware: mergeMiddleware(
+        [subagentSkillsMiddleware],
+        subagent.middleware || [],
+      ) as readonly AgentMiddleware[],
     };
   });
 
@@ -293,13 +294,15 @@ export function createDeepAgent<
    * Runtime middleware array: combine built-in + optional middleware
    * Note: The type is handled separately via AllMiddleware type alias
    */
-  const runtimeMiddleware: AgentMiddleware[] = [
-    ...builtInMiddleware,
-    ...skillsMiddlewareArray,
-    ...memoryMiddlewareArray,
-    ...(interruptOn ? [humanInTheLoopMiddleware({ interruptOn })] : []),
-    ...(customMiddleware as unknown as AgentMiddleware[]),
-  ];
+  const runtimeMiddleware: AgentMiddleware[] = mergeMiddleware(
+    [
+      ...builtInMiddleware,
+      ...skillsMiddlewareArray,
+      ...memoryMiddlewareArray,
+      ...(interruptOn ? [humanInTheLoopMiddleware({ interruptOn })] : []),
+    ],
+    customMiddleware as unknown as AgentMiddleware[],
+  );
 
   const agent = createAgent({
     model,
diff --git a/libs/deepagents/src/middleware/subagents.ts b/libs/deepagents/src/middleware/subagents.ts
index 53383c04b..cda233baf 100644
--- a/libs/deepagents/src/middleware/subagents.ts
+++ b/libs/deepagents/src/middleware/subagents.ts
@@ -17,6 +17,7 @@ import { Command, getCurrentTaskInput } from "@langchain/langgraph";
 import type { LanguageModelLike } from "@langchain/core/language_models/base";
 import type { Runnable } from "@langchain/core/runnables";
 import { HumanMessage } from "@langchain/core/messages";
+import { mergeMiddleware } from "./utils.js";
 
 export type { AgentMiddleware };
 
@@ -476,7 +477,7 @@ function getSubagents(options: {
       agents[agentParams.name] = agentParams.runnable;
     } else {
       const middleware = agentParams.middleware
-        ? [...defaultSubagentMiddleware, ...agentParams.middleware]
+        ? mergeMiddleware(defaultSubagentMiddleware, agentParams.middleware)
         : [...defaultSubagentMiddleware];
 
       const interruptOn = agentParams.interruptOn || defaultInterruptOn;
diff --git a/libs/deepagents/src/middleware/utils.test.ts b/libs/deepagents/src/middleware/utils.test.ts
index 0ad2c0eac..dcbf6fc24 100644
--- a/libs/deepagents/src/middleware/utils.test.ts
+++ b/libs/deepagents/src/middleware/utils.test.ts
@@ -1,6 +1,11 @@
 import { describe, it, expect } from "vitest";
 import { SystemMessage } from "@langchain/core/messages";
-import { appendToSystemMessage, prependToSystemMessage } from "./utils.js";
+import {
+  appendToSystemMessage,
+  prependToSystemMessage,
+  mergeMiddleware,
+} from "./utils.js";
+import { AgentMiddleware, MIDDLEWARE_BRAND } from "langchain";
 
 describe("appendToSystemMessage", () => {
   it("should create a new SystemMessage when original is null", () => {
@@ -94,3 +99,111 @@ describe("prependToSystemMessage", () => {
     });
   });
 });
+
+describe("mergeMiddleware", () => {
+  const createMockMiddleware = (name: string): AgentMiddleware => ({
+    [MIDDLEWARE_BRAND]: true,
+    name,
+  });
+
+  it("should return defaults when custom is empty", () => {
+    const defaults = [createMockMiddleware("mw1"), createMockMiddleware("mw2")];
+    const result = mergeMiddleware(defaults, []);
+    expect(result).toEqual(defaults);
+    expect(result).toHaveLength(2);
+  });
+
+  it("should return custom when defaults is empty", () => {
+    const custom = [createMockMiddleware("mw1"), createMockMiddleware("mw2")];
+    const result = mergeMiddleware([], custom);
+    expect(result).toEqual(custom);
+    expect(result).toHaveLength(2);
+  });
+
+  it("should return empty when both are empty", () => {
+    expect(mergeMiddleware([], [])).toEqual([]);
+  });
+
+  it("should replace default with same-named custom in-place", () => {
+    const mw1 = createMockMiddleware("mw1");
+    const mw2 = createMockMiddleware("mw2");
+    const mw3 = createMockMiddleware("mw3");
+    const mw2Override = createMockMiddleware("mw2");
+
+    const result = mergeMiddleware([mw1, mw2, mw3], [mw2Override]);
+
+    expect(result).toHaveLength(3);
+    expect(result[0]).toBe(mw1);
+    expect(result[1]).toBe(mw2Override); // replaced in-place
+    expect(result[2]).toBe(mw3);
+  });
+
+  it("should append custom middleware that has no default counterpart", () => {
+    const mw1 = createMockMiddleware("mw1");
+    const mw2 = createMockMiddleware("mw2");
+    const mw4 = createMockMiddleware("mw4");
+
+    const result = mergeMiddleware([mw1, mw2], [mw4]);
+
+    expect(result).toHaveLength(3);
+    expect(result[0]).toBe(mw1);
+    expect(result[1]).toBe(mw2);
+    expect(result[2]).toBe(mw4);
+  });
+
+  it("should handle mixed overrides and additions", () => {
+    const mw1 = createMockMiddleware("mw1");
+    const mw2 = createMockMiddleware("mw2");
+    const mw3 = createMockMiddleware("mw3");
+    const mw2Override = createMockMiddleware("mw2");
+    const mw4 = createMockMiddleware("mw4");
+
+    const result = mergeMiddleware([mw1, mw2, mw3], [mw2Override, mw4]);
+
+    expect(result).toHaveLength(4);
+    expect(result[0]).toBe(mw1);
+    expect(result[1]).toBe(mw2Override);
+    expect(result[2]).toBe(mw3);
+    expect(result[3]).toBe(mw4);
+  });
+
+  it("should replace all defaults when all are overridden", () => {
+    const mw1 = createMockMiddleware("mw1");
+    const mw2 = createMockMiddleware("mw2");
+    const mw1Override = createMockMiddleware("mw1");
+    const mw2Override = createMockMiddleware("mw2");
+
+    const result = mergeMiddleware([mw1, mw2], [mw1Override, mw2Override]);
+
+    expect(result).toHaveLength(2);
+    expect(result[0]).toBe(mw1Override);
+    expect(result[1]).toBe(mw2Override);
+  });
+
+  it("should preserve default order for non-overridden middleware", () => {
+    const mw1 = createMockMiddleware("mw1");
+    const mw2 = createMockMiddleware("mw2");
+    const mw3 = createMockMiddleware("mw3");
+    const mw1Override = createMockMiddleware("mw1");
+    const mw3Override = createMockMiddleware("mw3");
+
+    const result = mergeMiddleware([mw1, mw2, mw3], [mw3Override, mw1Override]);
+
+    expect(result).toHaveLength(3);
+    expect(result[0]).toBe(mw1Override);
+    expect(result[1]).toBe(mw2);
+    expect(result[2]).toBe(mw3Override);
+  });
+
+  it("should not mutate input arrays", () => {
+    const defaults = [createMockMiddleware("mw1"), createMockMiddleware("mw2")];
+    const custom = [createMockMiddleware("mw2"), createMockMiddleware("mw3")];
+    const defaultsCopy = [...defaults];
+    const customCopy = [...custom];
+
+    mergeMiddleware(defaults, custom);
+
+    expect(defaults).toEqual(defaultsCopy);
+    expect(custom).toEqual(customCopy);
+  });
+});
diff --git a/libs/deepagents/src/middleware/utils.ts b/libs/deepagents/src/middleware/utils.ts
index 1612954d9..2ba53e16d 100644
--- a/libs/deepagents/src/middleware/utils.ts
+++ b/libs/deepagents/src/middleware/utils.ts
@@ -5,6 +5,7 @@
  */
 
 import { SystemMessage } from "@langchain/core/messages";
+import { AgentMiddleware } from "langchain";
 
 /**
  * Append text to a system message.
@@ -94,3 +95,45 @@ export function prependToSystemMessage(
   // Fallback for unknown content type
   return new SystemMessage({ content: text });
 }
+
+/**
+ * Merge default and custom middleware arrays.
+ *
+ * Default middleware that share a name with a custom middleware are replaced
+ * in-place (preserving the default's position). Custom middleware that do not
+ * override any default are appended at the end.
+ *
+ * @param defaults - Base middleware array.
+ * @param custom - User-provided overrides and additions.
+ * @returns Merged middleware array with no duplicate names.
+ *
+ * @example
+ * ```typescript
+ * const defaults = [mw1, mw2, mw3];
+ * const custom   = [mw2Override, mw4];
+ * const result   = mergeMiddleware(defaults, custom);
+ * // Result: [mw1, mw2Override, mw3, mw4]
+ * ```
+ */
+export function mergeMiddleware(
+  defaults: readonly AgentMiddleware[],
+  custom: readonly AgentMiddleware[],
+): AgentMiddleware[] {
+  const customByName = new Map<string, AgentMiddleware>();
+  for (const mw of custom) {
+    customByName.set(mw.name, mw);
+  }
+
+  // Replace defaults in-place when a custom override exists
+  const merged = defaults.map((mw) => customByName.get(mw.name) ?? mw);
+
+  // Append custom middleware that didn't override any default
+  const defaultNames = new Set(defaults.map((mw) => mw.name));
+  for (const mw of custom) {
+    if (!defaultNames.has(mw.name)) {
+      merged.push(mw);
+    }
+  }
+
+  return merged;
+}