How to Override Claude Code's System Prompt (Complete Guide 2026)

Apr 1, 2026

The Problem: System Prompt Only Appends

When I tried to customize Claude Code’s behavior with a custom system prompt, I discovered something frustrating:

claude --system-prompt-file custom_instructions.md

I expected my custom instructions to replace Claude Code’s built-in system prompt. Instead, my instructions were appended to the end.

Here’s what actually happens:

[Claude Code's internal system prompt: ~10,000+ tokens]
+
[Your custom_instructions.md content]
=
[Combined prompt sent to Claude]

The problem: Claude Code has a sophisticated internal system prompt that defines:

Tool usage patterns (Read, Edit, Write, Bash, Glob, Grep)
Agent behaviors and decision-making logic
Safety guidelines and permission handling
MCP server integration rules

My custom instructions couldn’t override these core behaviors because they arrived at the weakest position in the prompt hierarchy.

The Prompt Hierarchy in Claude Code

I found a Reddit thread where developers were investigating this exact issue. One user discovered:

“Claude Code’s source confirms the system prompt problem - claude --system-prompt-file x appears only to append, not to replace, the actual system prompt seen by the Claude model.”

The hierarchy looks like this:

┌─────────────────────────────────────────────────────────────────────┐
│ Level 1: Internal System Prompt                                      │
│ Priority: Highest                                                    │
│ Can Override: NO (except via proxy workaround)                      │
│ Contains: Tool definitions, agent behaviors, safety rules           │
└─────────────────────────────────────────────────────────────────────┘
                              │
                              ▼
┌─────────────────────────────────────────────────────────────────────┐
│ Level 2: --system-prompt-file                                        │
│ Priority: Medium                                                     │
│ Can Override: Only appends to Level 1                                │
│ Contains: Your custom instructions                                   │
└─────────────────────────────────────────────────────────────────────┘
                              │
                              ▼
┌─────────────────────────────────────────────────────────────────────┐
│ Level 3: Managed/Project Settings                                     │
│ Priority: Medium-High                                                │
│ Can Override: Constraints only, not core behaviors                   │
│ Contains: Project-specific rules                                     │
└─────────────────────────────────────────────────────────────────────┘
                              │
                              ▼
┌─────────────────────────────────────────────────────────────────────┐
│ Level 4: CLAUDE.md                                                    │
│ Priority: Low                                                        │
│ Can Override: Context injection only                                 │
│ Contains: Project context and preferences                           │
└─────────────────────────────────────────────────────────────────────┘
                              │
                              ▼
┌─────────────────────────────────────────────────────────────────────┐
│ Level 5: User Message                                                │
│ Priority: Lowest                                                     │
│ Can Override: Request framing only                                   │
│ Contains: Your actual prompt                                        │
└─────────────────────────────────────────────────────────────────────┘

The Reddit thread revealed a key insight:

“CLAUDE.md is structurally subordinate to the system[] API parameter… arrives in a contradictory frame… occupies the weakest position in the prompt hierarchy.”

This explains why my CLAUDE.md couldn’t override core behaviors either.

The Solution: ANTHROPIC_BASE_URL Workaround

The same Reddit thread mentioned an unexpected workaround:

“Interestingly, setting ANTHROPIC_BASE_URL to a non-Anthropic service actually works correctly to override.”

This works because Claude Code has different behavior when connecting to Anthropic’s API vs. third-party endpoints.

How It Works

When Claude Code connects to Anthropic’s API directly, it injects its internal system prompt before your custom instructions. But when routing through a proxy or alternative endpoint, this injection behavior changes.

Here’s the setup:

export ANTHROPIC_BASE_URL=http://localhost:8080/v1
claude --system-prompt-file my_custom_prompt.md

The proxy intercepts requests and can:

Strip Claude Code’s internal system prompt
Inject your custom system prompt
Forward the request to Anthropic’s API

Building a Simple Proxy

I built a minimal proxy to test this:

from flask import Flask, request, Response
import requests
import os

app = Flask(__name__)

# Your custom system prompt
CUSTOM_SYSTEM_PROMPT = """
You are a specialized code assistant focused on Python development.
Always use type hints.
Prefer functional programming patterns.
Never use global state.
"""

ANTHROPIC_API_URL = "https://api.anthropic.com/v1/messages"

@app.route('/v1/messages', methods=['POST'])
def proxy():
    # Get the request body
    body = request.get_json()

    # Override the system prompt
    body['system'] = CUSTOM_SYSTEM_PROMPT

    # Forward to Anthropic
    headers = {
        'Content-Type': 'application/json',
        'x-api-key': os.environ.get('ANTHROPIC_API_KEY'),
        'anthropic-version': '2023-06-01'
    }

    response = requests.post(
        ANTHROPIC_API_URL,
        json=body,
        headers=headers
    )

    return Response(
        response.content,
        status=response.status_code,
        headers=dict(response.headers)
    )

if __name__ == '__main__':
    app.run(port=8080)

Then I started the proxy and connected Claude Code:

# Terminal 1: Start the proxy
export ANTHROPIC_API_KEY=your-key-here
python proxy.py

# Terminal 2: Connect Claude Code
export ANTHROPIC_BASE_URL=http://localhost:8080/v1
claude --system-prompt-file custom_instructions.md

Now my custom system prompt actually replaces the built-in one.

Testing the Override

To verify the override worked, I asked Claude what system prompt it received:

Me: What system prompt are you operating under?

Claude: I'm Claude, an AI assistant from Anthropic. I have access to various tools
including Read, Edit, Write, Bash, Glob, and Grep. I'm designed to help with
software development tasks like...
[Continues with standard Claude Code behavior]

Me: What system prompt are you operating under?

Claude: I am a specialized code assistant focused on Python development.
I always use type hints, prefer functional programming patterns,
and never use global state.
[Follows only my custom prompt]

The difference is clear: the proxy successfully replaced the system prompt.

Why This Matters

Understanding the prompt hierarchy and override methods matters for several use cases:

1. Custom Agent Behaviors

If you want Claude Code to follow specific coding standards or workflows that conflict with its default behavior, you need to override the system prompt.

Without override: Claude Code follows general software development patterns
With override: Claude Code follows your organization's specific patterns

2. Security and Compliance

Organizations may need to ensure Claude Code follows specific security guidelines:

Without override: Standard safety guidelines
With override: Organization-specific security protocols, data handling rules

3. Testing with Alternative Models

The proxy approach also enables testing with alternative models:

@app.route('/v1/messages', methods=['POST'])
def proxy():
    body = request.get_json()
    body['system'] = CUSTOM_SYSTEM_PROMPT

    # Route to alternative API instead of Anthropic
    response = requests.post(
        "https://alternative-api.com/v1/chat",
        json=body,
        headers=custom_headers
    )

    return Response(response.content, ...)

Limitations and Trade-offs

The ANTHROPIC_BASE_URL workaround isn’t perfect:

Aspect	Direct Connection	Proxy Override
System prompt control	Appends only	Full override
Tool definitions	Automatic	Must handle manually
Safety features	Built-in	Must reimplement
Setup complexity	None	Requires proxy
Performance	Optimal	Additional latency
Official support	Yes	No (workaround)

When using the proxy approach, you may need to:

Handle tool definitions manually if stripped
Reimplement any safety features you want to keep
Maintain the proxy infrastructure

The Reason: Why Claude Code Appends

Claude Code’s append-only behavior exists for practical reasons:

Tool Integration: The internal system prompt defines how Claude uses tools (Read, Edit, Write, Bash, etc.). Stripping this would break tool functionality.
Safety Guardrails: Built-in safety guidelines prevent dangerous operations. Removing them could allow harmful actions.
Consistent Behavior: Anthropic wants Claude Code to behave predictably across different users and projects.

The Reddit thread captured this tension:

“CLAUDE.md is structurally subordinate to the system[] API parameter… arrives in a contradictory frame… occupies the weakest position in the prompt hierarchy.”

The design prioritizes consistency and safety over customization. The ANTHROPIC_BASE_URL workaround exploits a side-effect: different handling for non-Anthropic endpoints.

Summary

In this post, I showed how to fully override Claude Code’s system prompt. The key points:

The problem: --system-prompt-file only appends, never replaces
The hierarchy: Internal system prompt has highest priority, CLAUDE.md has lowest
The solution: Setting ANTHROPIC_BASE_URL to a proxy endpoint enables full override
The trade-off: More control but more complexity and responsibility

For most users, appending via --system-prompt-file is sufficient. But when you need complete control over Claude Code’s behavior, the proxy approach is the only proven method.

The Reddit community discovered this through experimentation: “Multiple users tested this approach and confirmed that routing through a proxy service gives complete control over the system prompt.”

Final Words + More Resources

My intention with this article was to help others share my knowledge and experience. If you want to contact me, you can contact by email: Email me

Here are also the most important links from this article along with some further resources that will help you in this scope:

👨‍💻 Reddit Discussion: Claude Code's system prompt problem

Oh, and if you found these resources useful, don’t forget to support me by starring the repo on GitHub!