diff --git a/libs/deepagents/README.md b/libs/deepagents/README.md
index 003a33fd1..e20b81920 100644
--- a/libs/deepagents/README.md
+++ b/libs/deepagents/README.md
@@ -107,23 +107,6 @@ const agent = createDeepAgent({
 });
 ```
 
-A string is placed before the built-in Deep Agent prompt. For full control over
-prompt assembly, provide a structured configuration:
-
-```typescript
-const agent = createDeepAgent({
-  systemPrompt: {
-    prefix: "You are the support assistant for Acme.",
-    base: null, // Remove the built-in Deep Agent prompt.
-    suffix: "Follow Acme's escalation policy.",
-  },
-});
-```
-
-Structured prompts are assembled as `prefix` → `base` → `suffix`, followed by
-any model-specific harness profile suffix. Omit `base` to retain the active
-base prompt, or set it to `null` to remove the base entirely.
-
 See the [JavaScript Deep Agents docs](https://docs.langchain.com/oss/javascript/deepagents/overview) for full configuration options.
 
 ## LangGraph Native
diff --git a/libs/deepagents/src/agent.test-d.ts b/libs/deepagents/src/agent.test-d.ts
index 4a78aa5f1..5e6a0108f 100644
--- a/libs/deepagents/src/agent.test-d.ts
+++ b/libs/deepagents/src/agent.test-d.ts
@@ -21,7 +21,6 @@ import {
 import { StateSchema } from "@langchain/langgraph";
 import { z } from "zod/v4";
 import { createDeepAgent } from "./agent.js";
-import type { SystemPromptConfig } from "./index.js";
 import type {
   MergedDeepAgentState,
   InferSubagentByName,
@@ -78,50 +77,23 @@ const MemoryMiddleware = createMiddleware({
 });
 
 describe("createDeepAgent types", () => {
-  it("should allow legacy and structured system prompts", () => {
+  it("should allow systemPrompt to be a string or SystemMessage", () => {
     createDeepAgent({
       systemPrompt: "Hello, world!",
     });
-    const message = new SystemMessage({
-      content: [
-        {
-          type: "text",
-          text: "Hello, world!",
-        },
-      ],
-    });
-    createDeepAgent({ systemPrompt: message });
-    createDeepAgent({ systemPrompt: {} });
-    createDeepAgent({
-      systemPrompt: {
-        prefix: message,
-        base: null,
-        suffix: "Follow the policy.",
-      },
-    });
-
-    const config: SystemPromptConfig = {
-      prefix: null,
-      base: message,
-      suffix: null,
-    };
-    createDeepAgent({ systemPrompt: config });
-
     createDeepAgent({
-      // @ts-expect-error systemPrompt does not accept numbers
-      systemPrompt: 42,
-    });
-    createDeepAgent({
-      systemPrompt: {
-        // @ts-expect-error prompt parts do not accept numbers
-        prefix: 42,
-      },
+      systemPrompt: new SystemMessage({
+        content: [
+          {
+            type: "text",
+            text: "Hello, world!",
+          },
+        ],
+      }),
     });
     createDeepAgent({
-      systemPrompt: {
-        // @ts-expect-error unknown structured prompt field
-        unknownField: "value",
-      },
+      // @ts-expect-error systemPrompt does not accept structured configurations
+      systemPrompt: { base: null },
     });
   });
 
diff --git a/libs/deepagents/src/agent.test.ts b/libs/deepagents/src/agent.test.ts
index 3475404c2..67b29697f 100644
--- a/libs/deepagents/src/agent.test.ts
+++ b/libs/deepagents/src/agent.test.ts
@@ -1,6 +1,5 @@
 import { describe, it, expect, vi } from "vitest";
 import { createDeepAgent } from "./agent.js";
-import type { SystemPromptConfig } from "./types.js";
 import { isAnthropicModel } from "./utils.js";
 import { FakeListChatModel } from "@langchain/core/utils/testing";
 import {
@@ -12,10 +11,7 @@ import { MemorySaver, StateSchema } from "@langchain/langgraph";
 import { createFileData } from "./backends/utils.js";
 import { ConfigurationError } from "./errors.js";
 import { assertAllDeepAgentQualities } from "./testing/utils.js";
-import {
-  _resetRegistryForTesting,
-  registerHarnessProfile,
-} from "./profiles/harness/index.js";
+import { registerHarnessProfile } from "./profiles/harness/index.js";
 import { z } from "zod/v4";
 
 describe("isAnthropicModel", () => {
@@ -64,7 +60,7 @@ describe("isAnthropicModel", () => {
   });
 });
 
-describe("Structured system prompt configuration", () => {
+describe("Legacy system prompt assembly", () => {
   function getLastSystemMessage(
     invokeSpy: ReturnType<typeof vi.spyOn>,
   ): SystemMessage {
@@ -79,167 +75,64 @@ describe("Structured system prompt configuration", () => {
     return systemMessage;
   }
 
-  it("assembles configured prompt parts in order", async () => {
+  it("separates a string system prompt from the base prompt", async () => {
     const invokeSpy = vi.spyOn(FakeListChatModel.prototype, "invoke");
-    const cases: Array<{
-      systemPrompt: string | SystemPromptConfig;
-      ordered: string[];
-      absent?: string[];
-    }> = [
-      {
-        systemPrompt: {},
-        ordered: ["You are a Deep Agent"],
-      },
-      {
-        systemPrompt: { base: "__base__" },
-        ordered: ["__base__"],
-        absent: ["You are a Deep Agent"],
-      },
-      {
-        systemPrompt: { prefix: "__prefix__" },
-        ordered: ["__prefix__", "You are a Deep Agent"],
-      },
-      {
-        systemPrompt: { suffix: "__suffix__" },
-        ordered: ["You are a Deep Agent", "__suffix__"],
-      },
-      {
-        systemPrompt: {
-          prefix: "__prefix__",
-          base: "__base__",
-          suffix: "__suffix__",
-        },
-        ordered: ["__prefix__", "__base__", "__suffix__"],
-        absent: ["You are a Deep Agent"],
-      },
-      {
-        systemPrompt: { base: null, suffix: "__only__" },
-        ordered: ["__only__"],
-        absent: ["You are a Deep Agent"],
-      },
-      {
-        systemPrompt: "__legacy__",
-        ordered: ["__legacy__", "You are a Deep Agent"],
-      },
-    ];
 
     try {
-      for (const testCase of cases) {
-        const model = new FakeListChatModel({ responses: ["Done"] });
-        const agent = createDeepAgent({
-          model,
-          systemPrompt: testCase.systemPrompt,
-        });
-        await agent.invoke({ messages: [new HumanMessage("Hello")] });
-
-        const text = getLastSystemMessage(invokeSpy).text;
-        const positions = testCase.ordered.map((fragment) =>
-          text.indexOf(fragment),
-        );
-        expect(positions.every((position) => position >= 0)).toBe(true);
-        expect(positions).toEqual([...positions].sort((a, b) => a - b));
-        for (const fragment of testCase.absent ?? []) {
-          expect(text).not.toContain(fragment);
-        }
-      }
+      const agent = createDeepAgent({
+        model: new FakeListChatModel({ responses: ["Done"] }),
+        systemPrompt: "__custom_prompt__",
+      });
+      await agent.invoke({ messages: [new HumanMessage("Hello")] });
+
+      const prompt = getLastSystemMessage(invokeSpy).text;
+      expect(prompt).toContain("__custom_prompt__\n\nYou are a Deep Agent");
     } finally {
       invokeSpy.mockRestore();
     }
   });
 
-  it("preserves SystemMessage content blocks and cache control", async () => {
+  it("preserves SystemMessage content blocks before the base prompt", async () => {
     const invokeSpy = vi.spyOn(FakeListChatModel.prototype, "invoke");
-    const cachedPrefix = new SystemMessage({
+    const customPrompt = new SystemMessage({
       content: [
         {
           type: "text",
-          text: "__cached_prefix__",
+          text: "__cached_custom_prompt__",
           cache_control: { type: "ephemeral" },
         },
       ],
     });
 
     try {
-      const model = new FakeListChatModel({ responses: ["Done"] });
       const agent = createDeepAgent({
-        model,
-        systemPrompt: { prefix: cachedPrefix, suffix: "__suffix__" },
+        model: new FakeListChatModel({ responses: ["Done"] }),
+        systemPrompt: customPrompt,
       });
       await agent.invoke({ messages: [new HumanMessage("Hello")] });
 
       const blocks = getLastSystemMessage(invokeSpy).contentBlocks;
-      const cachedBlock = blocks.find(
-        (block) => block.type === "text" && block.text === "__cached_prefix__",
+      const customIndex = blocks.findIndex(
+        (block) =>
+          block.type === "text" && block.text === "__cached_custom_prompt__",
       );
-      expect(cachedBlock?.cache_control).toEqual({ type: "ephemeral" });
-      expect(blocks.filter((block) => block.type === "text")).toEqual(
-        expect.arrayContaining([
-          expect.objectContaining({ text: "\n\n" }),
-          expect.objectContaining({ text: "__suffix__" }),
-        ]),
+      const baseIndex = blocks.findIndex(
+        (block) =>
+          block.type === "text" && block.text.includes("You are a Deep Agent"),
       );
-      const text = getLastSystemMessage(invokeSpy).text;
-      expect(text.indexOf("__cached_prefix__")).toBeLessThan(
-        text.indexOf("You are a Deep Agent"),
-      );
-      expect(text.indexOf("You are a Deep Agent")).toBeLessThan(
-        text.indexOf("__suffix__"),
-      );
-    } finally {
-      invokeSpy.mockRestore();
-    }
-  });
 
-  it("gives configured base precedence over the harness profile base", async () => {
-    _resetRegistryForTesting();
-    registerHarnessProfile("openai", {
-      baseSystemPrompt: "__profile_base__",
-      systemPromptSuffix: "__profile_suffix__",
-    });
-    const invokeSpy = vi.spyOn(FakeListChatModel.prototype, "invoke");
-
-    async function invokeWithPrompt(
-      systemPrompt: SystemPromptConfig,
-    ): Promise<string> {
-      const model = new FakeListChatModel({ responses: ["Done"] });
-      vi.spyOn(model, "getName").mockReturnValue("ChatOpenAI");
-      const agent = createDeepAgent({ model, systemPrompt });
-      await agent.invoke({ messages: [new HumanMessage("Hello")] });
-      return getLastSystemMessage(invokeSpy).text;
-    }
-
-    try {
-      const profileBaseText = await invokeWithPrompt({ suffix: "__suffix__" });
-      expect(profileBaseText.indexOf("__profile_base__")).toBeLessThan(
-        profileBaseText.indexOf("__suffix__"),
-      );
-      expect(profileBaseText.indexOf("__suffix__")).toBeLessThan(
-        profileBaseText.indexOf("__profile_suffix__"),
-      );
-
-      const configuredBaseText = await invokeWithPrompt({
-        base: "__configured_base__",
-        suffix: "__suffix__",
+      expect(blocks[customIndex]?.cache_control).toEqual({
+        type: "ephemeral",
       });
-      expect(configuredBaseText).not.toContain("__profile_base__");
-      expect(configuredBaseText.indexOf("__configured_base__")).toBeLessThan(
-        configuredBaseText.indexOf("__suffix__"),
-      );
-      expect(configuredBaseText.indexOf("__suffix__")).toBeLessThan(
-        configuredBaseText.indexOf("__profile_suffix__"),
-      );
-
-      const noBaseText = await invokeWithPrompt({
-        base: null,
-        suffix: "__suffix__",
-      });
-      expect(noBaseText).not.toContain("__profile_base__");
-      expect(noBaseText.indexOf("__suffix__")).toBeLessThan(
-        noBaseText.indexOf("__profile_suffix__"),
+      expect(customIndex).toBeLessThan(baseIndex);
+      expect(blocks[baseIndex]).toEqual(
+        expect.objectContaining({
+          type: "text",
+          text: expect.stringMatching(/^\n\n/),
+        }),
       );
     } finally {
       invokeSpy.mockRestore();
-      _resetRegistryForTesting();
     }
   });
 });
diff --git a/libs/deepagents/src/agent.ts b/libs/deepagents/src/agent.ts
index b4db1906c..a2869d4ea 100644
--- a/libs/deepagents/src/agent.ts
+++ b/libs/deepagents/src/agent.ts
@@ -47,7 +47,6 @@ import type {
   FlattenSubAgentMiddleware,
   InferStructuredResponse,
   SupportedResponseFormat,
-  SystemPromptConfig,
 } from "./types.js";
 /**
  * required for type inference
@@ -103,52 +102,6 @@ const BASE_AGENT_PROMPT = context`
   For longer tasks, provide brief progress updates at reasonable intervals — a concise sentence recapping what you've done and what's next.
 `;
 
-const PROMPT_SEPARATOR = "\n\n";
-
-type SystemPromptPart = string | SystemMessage;
-type SystemPromptContentBlock = SystemMessage["contentBlocks"][number];
-
-/** Normalize legacy system prompt values to the structured representation. */
-function normalizeSystemPrompt(
-  systemPrompt: SystemPromptPart | SystemPromptConfig | undefined,
-): SystemPromptConfig {
-  if (systemPrompt === undefined) {
-    return {};
-  }
-  if (
-    typeof systemPrompt === "string" ||
-    SystemMessage.isInstance(systemPrompt)
-  ) {
-    return { prefix: systemPrompt };
-  }
-  return systemPrompt;
-}
-
-/** Assemble prompt parts while preserving structured message content blocks. */
-function assemblePromptParts(
-  parts: readonly SystemPromptPart[],
-): string | SystemMessage {
-  if (parts.length === 0) {
-    return "";
-  }
-  if (parts.every((part) => typeof part === "string")) {
-    return parts.join(PROMPT_SEPARATOR);
-  }
-
-  const contentBlocks: SystemPromptContentBlock[] = [];
-  for (const [index, part] of parts.entries()) {
-    if (index > 0) {
-      contentBlocks.push({ type: "text", text: PROMPT_SEPARATOR });
-    }
-    if (SystemMessage.isInstance(part)) {
-      contentBlocks.push(...part.contentBlocks);
-    } else {
-      contentBlocks.push({ type: "text", text: part });
-    }
-  }
-  return new SystemMessage({ contentBlocks });
-}
-
 const BUILTIN_TOOL_NAMES: ReadonlySet<string> = new Set([
   ...FILESYSTEM_TOOL_NAMES,
   ...ASYNC_TASK_TOOL_NAMES,
@@ -501,31 +454,38 @@ export function createDeepAgent<
     );
   }
 
-  // Assemble the main-agent prompt in this order:
-  // caller prefix -> active base -> caller suffix -> profile suffix.
-  const promptConfig = normalizeSystemPrompt(systemPrompt);
-  const promptParts: SystemPromptPart[] = [];
-
-  if (promptConfig.prefix !== undefined && promptConfig.prefix !== null) {
-    promptParts.push(promptConfig.prefix);
-  }
-
-  const activeBasePrompt =
-    promptConfig.base !== undefined
-      ? promptConfig.base
-      : (harnessProfile.baseSystemPrompt ?? BASE_AGENT_PROMPT);
-  if (activeBasePrompt !== null) {
-    promptParts.push(activeBasePrompt);
-  }
-
-  if (promptConfig.suffix) {
-    promptParts.push(promptConfig.suffix);
-  }
-  if (harnessProfile.systemPromptSuffix) {
-    promptParts.push(harnessProfile.systemPromptSuffix);
-  }
+  // Combine system prompt parameter with profile-aware base prompt.
+  const effectiveBasePrompt = applyProfilePrompt(
+    harnessProfile,
+    BASE_AGENT_PROMPT,
+  );
 
-  const finalSystemPrompt = assemblePromptParts(promptParts);
+  const basePromptBlocks = effectiveBasePrompt
+    ? ([
+        {
+          type: "text" as const,
+          text: `\n\n${effectiveBasePrompt}`,
+        },
+      ] as const)
+    : [];
+
+  const finalSystemPrompt =
+    typeof systemPrompt === "string"
+      ? new SystemMessage({
+          contentBlocks: [
+            { type: "text", text: systemPrompt },
+            ...basePromptBlocks,
+          ],
+        })
+      : SystemMessage.isInstance(systemPrompt)
+        ? new SystemMessage({
+            contentBlocks: [...systemPrompt.contentBlocks, ...basePromptBlocks],
+          })
+        : new SystemMessage({
+            contentBlocks: effectiveBasePrompt
+              ? [{ type: "text", text: effectiveBasePrompt }]
+              : [],
+          });
 
   const agent = createAgent({
     model,
diff --git a/libs/deepagents/src/browser.ts b/libs/deepagents/src/browser.ts
index daf4ed698..7db4d9b39 100644
--- a/libs/deepagents/src/browser.ts
+++ b/libs/deepagents/src/browser.ts
@@ -32,7 +32,6 @@ export type { DeepAgentRunStream, SubagentRunStream } from "./stream.js";
 export type {
   AnySubAgent,
   CreateDeepAgentParams,
-  SystemPromptConfig,
   MergedDeepAgentState,
   // DeepAgent type bag and helper types
   DeepAgent,
diff --git a/libs/deepagents/src/index.ts b/libs/deepagents/src/index.ts
index 01317b16e..d8a5f5296 100644
--- a/libs/deepagents/src/index.ts
+++ b/libs/deepagents/src/index.ts
@@ -29,7 +29,6 @@ export type { DeepAgentRunStream, SubagentRunStream } from "./stream.js";
 export type {
   AnySubAgent,
   CreateDeepAgentParams,
-  SystemPromptConfig,
   MergedDeepAgentState,
   // DeepAgent type bag and helper types
   DeepAgent,
diff --git a/libs/deepagents/src/profiles/harness/registry.test.ts b/libs/deepagents/src/profiles/harness/registry.test.ts
index 53f0e7902..f26d9ee67 100644
--- a/libs/deepagents/src/profiles/harness/registry.test.ts
+++ b/libs/deepagents/src/profiles/harness/registry.test.ts
@@ -145,6 +145,14 @@ describe("applyProfilePrompt", () => {
       "New base.\n\nAnd a suffix.",
     );
   });
+
+  it("uses a suffix without a leading separator when the base is empty", () => {
+    const profile = createHarnessProfile({
+      baseSystemPrompt: "",
+      systemPromptSuffix: "Suffix only.",
+    });
+    expect(applyProfilePrompt(profile, "Default prompt.")).toBe("Suffix only.");
+  });
 });
 
 describe("resolveHarnessProfile", () => {
diff --git a/libs/deepagents/src/profiles/harness/registry.ts b/libs/deepagents/src/profiles/harness/registry.ts
index d5ae0477a..6dbd8fddb 100644
--- a/libs/deepagents/src/profiles/harness/registry.ts
+++ b/libs/deepagents/src/profiles/harness/registry.ts
@@ -301,7 +301,9 @@ export function applyProfilePrompt(
       ? profile.baseSystemPrompt
       : basePrompt;
   if (profile.systemPromptSuffix !== undefined) {
-    return `${prompt}\n\n${profile.systemPromptSuffix}`;
+    return prompt
+      ? `${prompt}\n\n${profile.systemPromptSuffix}`
+      : profile.systemPromptSuffix;
   }
   return prompt;
 }
diff --git a/libs/deepagents/src/types.ts b/libs/deepagents/src/types.ts
index d66942789..a4ec033c4 100644
--- a/libs/deepagents/src/types.ts
+++ b/libs/deepagents/src/types.ts
@@ -488,28 +488,6 @@ export type InferSubagentReactAgentType<
       >
     : never;
 
-/**
- * Structured system prompt configuration for {@link createDeepAgent}.
- *
- * Prompt parts are assembled in the order `prefix` → `base` → `suffix`,
- * followed by any model-specific harness profile suffix.
- */
-export interface SystemPromptConfig {
-  /** Content placed before the base prompt. */
-  prefix?: string | SystemMessage | null;
-
-  /**
-   * Replacement for the active base prompt.
-   *
-   * Omit this field to retain the harness profile base or built-in base prompt.
-   * Set it to `null` to omit the base prompt entirely.
-   */
-  base?: string | SystemMessage | null;
-
-  /** Content placed after the base prompt and before any harness profile suffix. */
-  suffix?: string | SystemMessage | null;
-}
-
 /**
  * Configuration parameters for creating a Deep Agent
  * Matches Python's create_deep_agent parameters
@@ -541,14 +519,8 @@ export interface CreateDeepAgentParams<
   model?: BaseLanguageModel | string;
   /** Tools the agent should have access to */
   tools?: TTools | StructuredTool[];
-  /**
-   * Custom system instructions for the agent.
-   *
-   * A string or {@link SystemMessage} is placed before the active base prompt.
-   * For more control, provide a {@link SystemPromptConfig} to replace or remove
-   * the base prompt and add content after it.
-   */
-  systemPrompt?: string | SystemMessage | SystemPromptConfig;
+  /** Custom system prompt for the agent. This will be combined with the base agent prompt */
+  systemPrompt?: string | SystemMessage;
   /**
    * Optional schema for custom agent state. Allows you to define custom state properties
    * beyond built-in `messages`, `todos`, and `files`. These properties can be accessed