# 2457 Agent Sdk Modifying System Prompts 80194168

> System prompts define Claude's behavior, capabilities, and response style. The Claude Agent SDK provides three ways to customize system prompts: using output styles (persistent, file-based configurations), appending to Claude Code's prompt, or using a fully custom prompt.

- Skill: `tools-only/2457-agent-sdk-modifying-system-prompts-80194168` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add tools-only/2457-agent-sdk-modifying-system-prompts-80194168`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tools-only/2457-agent-sdk-modifying-system-prompts-80194168/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: tools-only (https://skillmd.com/u/tools-only)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/tools-only/2457-agent-sdk-modifying-system-prompts-80194168

---


System prompts define Claude's behavior, capabilities, and response style. The Claude Agent SDK provides three ways to customize system prompts: using output styles (persistent, file-based configurations), appending to Claude Code's prompt, or using a fully custom prompt.

## Understanding system prompts

A system prompt is the initial instruction set that shapes how Claude behaves throughout a conversation.

**Default behavior:** The Agent SDK uses an **empty system prompt** by default for maximum flexibility. To use Claude Code's system prompt (tool instructions, code guidelines, etc.), specify `systemPrompt: { preset: "claude_code" }` in TypeScript or `system_prompt="claude_code"` in Python.

Claude Code's system prompt includes:

- Tool usage instructions and available tools
- Code style and formatting guidelines
- Response tone and verbosity settings
- Security and safety instructions
- Context about the current working directory and environment

## Methods of modification

### Method 1: CLAUDE.md files (project-level instructions)

CLAUDE.md files provide project-specific context and instructions that are automatically read by the Agent SDK when it runs in a directory. They serve as persistent "memory" for your project.

#### How CLAUDE.md works with the SDK

**Location and discovery:**

- **Project-level:** `CLAUDE.md` or `.claude/CLAUDE.md` in your working directory
- **User-level:** `~/.claude/CLAUDE.md` for global instructions across all projects

**IMPORTANT:** The SDK only reads CLAUDE.md files when you explicitly configure `settingSources` (TypeScript) or `setting_sources` (Python):

- Include `'project'` to load project-level CLAUDE.md
- Include `'user'` to load user-level CLAUDE.md (`~/.claude/CLAUDE.md`)

The `claude_code` system prompt preset does NOT automatically load CLAUDE.md - you must also specify setting sources.

**Content format:** CLAUDE.md files use plain markdown and can contain:

- Coding guidelines and standards
- Project-specific context
- Common commands or workflows
- API conventions
- Testing requirements

#### Example CLAUDE.md

    # Project Guidelines

    ## Code Style

    - Use TypeScript strict mode
    - Prefer functional components in React
    - Always include JSDoc comments for public APIs

    ## Testing

    - Run `npm test` before committing
    - Maintain >80% code coverage
    - Use jest for unit tests, playwright for E2E

    ## Commands

    - Build: `npm run build`
    - Dev server: `npm run dev`
    - Type check: `npm run typecheck`

#### Using CLAUDE.md with the SDK

    import { query } from "@anthropic-ai/claude-agent-sdk";

    // IMPORTANT: You must specify settingSources to load CLAUDE.md
    // The claude_code preset alone does NOT load CLAUDE.md files
    const messages = [];

    for await (const message of query({
      prompt: "Add a new React component for user profiles",
      options: {
        systemPrompt: {
          type: "preset",
          preset: "claude_code", // Use Claude Code's system prompt
        },
        settingSources: ["project"], // Required to load CLAUDE.md from project
      },
    })) {
      messages.push(message);
    }

    // Now Claude has access to your project guidelines from CLAUDE.md

#### When to use CLAUDE.md

**Best for:**

- **Team-shared context** - Guidelines everyone should follow
- **Project conventions** - Coding standards, file structure, naming patterns
- **Common commands** - Build, test, deploy commands specific to your project
- **Long-term memory** - Context that should persist across all sessions
- **Version-controlled instructions** - Commit to git so the team stays in sync

**Key characteristics:**

- ✅ Persistent across all sessions in a project
- ✅ Shared with team via git
- ✅ Automatic discovery (no code changes needed)
- ⚠️ Requires loading settings via `settingSources`

### Method 2: Output styles (persistent configurations)

Output styles are saved configurations that modify Claude's system prompt. They're stored as markdown files and can be reused across sessions and projects.

#### Creating an output style

    import { writeFile, mkdir } from "fs/promises";
    import { join } from "path";
    import { homedir } from "os";

    async function createOutputStyle(
      name: string,
      description: string,
      prompt: string
    ) {
      // User-level: ~/.claude/output-styles
      // Project-level: .claude/output-styles
      const outputStylesDir = join(homedir(), ".claude", "output-styles");

      await mkdir(outputStylesDir, { recursive: true });

      const content = `---
    name: ${name}
    description: ${description}
    ---

    ${prompt}`;

      const filePath = join(
        outputStylesDir,
        `${name.toLowerCase().replace(/\s+/g, "-")}.md`
      );
      await writeFile(filePath, content, "utf-8");
    }

    // Example: Create a code review specialist
    await createOutputStyle(
      "Code Reviewer",
      "Thorough code review assistant",
      `You are an expert code reviewer.

    For every code submission:
    1. Check for bugs and security issues
    2. Evaluate performance
    3. Suggest improvements
    4. Rate code quality (1-10)`
    );

#### Using output styles

Once created, activate output styles via:

- **CLI**: `/output-style [style-name]`
- **Settings**: `.claude/settings.local.json`
- **Create new**: `/output-style:new [description]`

**Note for SDK users:** Output styles are loaded when you include `settingSources: ['user']` or `settingSources: ['project']` (TypeScript) / `setting_sources=["user"]` or `setting_sources=["project"]` (Python) in your options.

### Method 3: Using `systemPrompt` with append

You can use the Claude Code preset with an `append` property to add your custom instructions while preserving all built-in functionality.

    import { query } from "@anthropic-ai/claude-agent-sdk";

    const messages = [];

    for await (const message of query({
      prompt: "Help me write a Python function to calculate fibonacci numbers",
      options: {
        systemPrompt: {
          type: "preset",
          preset: "claude_code",
          append:
            "Always include detailed docstrings and type hints in Python code.",
        },
      },
    })) {
      messages.push(message);
      if (message.type === "assistant") {
        console.log(message.message.content);
      }
    }

### Method 4: Custom system prompts

You can provide a custom string as `systemPrompt` to replace the default entirely with your own instructions.

    import { query } from "@anthropic-ai/claude-agent-sdk";

    const customPrompt = `You are a Python coding specialist.
    Follow these guidelines:
    - Write clean, well-documented code
    - Use type hints for all functions
    - Include comprehensive docstrings
    - Prefer functional programming patterns when appropriate
    - Always explain your code choices`;

    const messages = [];

    for await (const message of query({
      prompt: "Create a data processing pipeline",
      options: {
        systemPrompt: customPrompt,
      },
    })) {
      messages.push(message);
      if (message.type === "assistant") {
        console.log(message.message.content);
      }
    }

## Comparison of all four approaches

| Feature | CLAUDE.md | Output Styles | `systemPrompt` with append | Custom `systemPrompt` |
|----|----|----|----|----|
| **Persistence** | Per-project file | Saved as files | Session only | Session only |
| **Reusability** | Per-project | Across projects | Code duplication | Code duplication |
| **Management** | On filesystem | CLI + files | In code | In code |
| **Default tools** | Preserved | Preserved | Preserved | Lost (unless included) |
| **Built-in safety** | Maintained | Maintained | Maintained | Must be added |
| **Environment context** | Automatic | Automatic | Automatic | Must be provided |
| **Customization level** | Additions only | Replace default | Additions only | Complete control |
| **Version control** | With project | Yes | With code | With code |
| **Scope** | Project-specific | User or project | Code session | Code session |

**Note:** "With append" means using `systemPrompt: { type: "preset", preset: "claude_code", append: "..." }` in TypeScript or `system_prompt={"type": "preset", "preset": "claude_code", "append": "..."}` in Python.

## Use cases and best practices

### When to use CLAUDE.md

**Best for:**

- Project-specific coding standards and conventions
- Documenting project structure and architecture
- Listing common commands (build, test, deploy)
- Team-shared context that should be version controlled
- Instructions that apply to all SDK usage in a project

**Examples:**

- "All API endpoints should use async/await patterns"
- "Run `npm run lint:fix` before committing"
- "Database migrations are in the `migrations/` directory"

**Important:** To load CLAUDE.md files, you must explicitly set `settingSources: ['project']` (TypeScript) or `setting_sources=["project"]` (Python). The `claude_code` system prompt preset does NOT automatically load CLAUDE.md without this setting.

### When to use output styles

**Best for:**

- Persistent behavior changes across sessions
- Team-shared configurations
- Specialized assistants (code reviewer, data scientist, DevOps)
- Complex prompt modifications that need versioning

**Examples:**

- Creating a dedicated SQL optimization assistant
- Building a security-focused code reviewer
- Developing a teaching assistant with specific pedagogy

### When to use `systemPrompt` with append

**Best for:**

- Adding specific coding standards or preferences
- Customizing output formatting
- Adding domain-specific knowledge
- Modifying response verbosity
- Enhancing Claude Code's default behavior without losing tool instructions

### When to use custom `systemPrompt`

**Best for:**

- Complete control over Claude's behavior
- Specialized single-session tasks
- Testing new prompt strategies
- Situations where default tools aren't needed
- Building specialized agents with unique behavior

## Combining approaches

You can combine these methods for maximum flexibility:

### Example: Output style with session-specific additions

    import { query } from "@anthropic-ai/claude-agent-sdk";

    // Assuming "Code Reviewer" output style is active (via /output-style)
    // Add session-specific focus areas
    const messages = [];

    for await (const message of query({
      prompt: "Review this authentication module",
      options: {
        systemPrompt: {
          type: "preset",
          preset: "claude_code",
          append: `
            For this review, prioritize:
            - OAuth 2.0 compliance
            - Token storage security
            - Session management
          `,
        },
      },
    })) {
      messages.push(message);
    }

## See also

- [Output styles](https://code.claude.com/docs/en/output-styles) - Complete output styles documentation
- [TypeScript SDK guide](https://platform.claude.com/docs/en/agent-sdk/typescript) - Complete SDK usage guide
- [Configuration guide](https://code.claude.com/docs/en/settings) - General configuration options