SDK vs CLI System Prompts

When sending the same message through the Claude Agent SDK versus the Claude CLI (Claude Code), the system prompts accompanying these messages are fundamentally different. There is no guarantee of identical output between the two, even with matching configurations, due to the absence of a seed parameter and inherent non-determinism in Claude’s architecture.

System Prompt Comparison

Claude CLI (Claude Code)

The Claude CLI uses a modular system prompt architecture with a ~269-token base prompt, with additional context conditionally loaded: | Component | Description | Loading | |-----------|-------------|---------|| | Base System Prompt | Core instructions and behavior | Always (~269 tokens) | | Tool Instructions | 18+ builtin tools (Write, Read, Edit, Bash, TodoWrite, etc.) | Always | | Coding Guidelines | Code style, formatting rules, security practices | Always | | Safety Rules | Refusal rules, injection defense, harm prevention | Always | | Response Style | Tone, verbosity, explanation depth, emoji usage | Always | | Environment Context | Working directory, git status, platform info | Always | | Project Context | CLAUDE.md content, settings, hooks configuration | Conditional | | Subagent Prompts | Plan mode, Explore agent, Task agent | Conditional | | Security Review | Extended security instructions (~2,610 tokens) | Conditional |

Key Characteristics

Modular architecture with 110+ system prompt strings loaded conditionally
Base prompt is modest (~269 tokens), total varies by features activated
Includes extensive security and injection defense layers
Automatically loads CLAUDE.md files in the working directory
Session-persistent context in interactive mode

Claude Agent SDK

The Agent SDK uses a minimal system prompt by default containing: | Component | Description | Token Impact | |-----------|-------------|--------------|| | Essential Tool Instructions | Only tools explicitly provided | Minimal | | Basic Safety | Minimal safety instructions | Minimal |

Key Characteristics

No coding guidelines or style preferences by default
No project context unless explicitly configured
No extensive tool descriptions
Requires explicit configuration to match CLI behavior

What Each Interface Sends

Example: “What is the capital of Norway?”

Via Claude CLI
Via SDK (Default)
Via SDK (with preset)

System Prompt: [modular, ~269+ base tokens]
├── Base system prompt (~269 tokens)
├── Tool instructions (Write, Read, Edit, Bash, Grep, Glob, etc.)
├── Git safety protocols
├── Code reference guidelines
├── Professional objectivity instructions
├── Security and injection defense rules
├── Environment context (OS, directory, date)
├── CLAUDE.md content (if present) [conditional]
├── MCP tool descriptions (if configured) [conditional]
├── Plan/Explore mode prompts [conditional]
└── Session/conversation context

User Message: "What is the capital of Norway?"

System Prompt: [minimal]
├── Essential tool instructions (if any tools provided)
└── Basic operational context

User Message: "What is the capital of Norway?"

const response = await query({
  prompt: "What is the capital of Norway?",
  options: {
    systemPrompt: {
      type: "preset",
      preset: "claude_code"
    }
  }
});

System Prompt: [modular, matches CLI]
├── Full Claude Code system prompt
├── Tool instructions
├── Coding guidelines
└── Safety rules

// NOTE: Still does NOT include CLAUDE.md unless settingSources is configured

Customization Methods

Claude CLI Customization

Method	Command	Effect
Append to prompt	`claude -p "..." --append-system-prompt "..."`	Adds instructions while preserving defaults
Replace prompt	`claude -p "..." --system-prompt "..."`	Completely replaces the system prompt
Project context	CLAUDE.md file	Automatically loaded, persistent
Output styles	`/output-style [name]`	Apply predefined response styles

Agent SDK Customization

Method	Configuration	Effect
Custom prompt	`systemPrompt: "..."`	Replaces default entirely (loses tools)
Preset with append	`systemPrompt: { type: "preset", preset: "claude_code", append: "..." }`	Preserves CLI functionality + custom instructions
CLAUDE.md loading	`settingSources: ["project"]`	Loads project-level instructions
Output styles	`settingSources: ["user"]` or `settingSources: ["project"]`	Loads saved output styles

Configuration Comparison

| Feature | CLI Default | SDK Default | SDK with Preset | |---------|-------------|-------------|-----------------|| | Tool instructions | ✅ Full | ❌ Minimal | ✅ Full | | Coding guidelines | ✅ Yes | ❌ No | ✅ Yes | | Safety rules | ✅ Yes | ❌ Basic | ✅ Yes | | CLAUDE.md auto-load | ✅ Yes | ❌ No | ❌ No* | | Project context | ✅ Automatic | ❌ No | ❌ No* |

*Requires explicit settingSources: ["project"] configuration

Output Consistency Guarantees

Critical Finding: NO Determinism GuaranteedThe Claude Messages API does not provide a seed parameter for reproducibility. This is a fundamental architectural limitation.

Factors Preventing Identical Output

| Factor | Description | Controllable? | |--------|-------------|---------------|| | Different system prompts | CLI vs SDK have different defaults | ✅ Yes (with configuration) | | Floating-point arithmetic | Parallel hardware quirks | ❌ No | | MoE routing | Mixture-of-Experts architecture variations | ❌ No | | Batching/scheduling | Cloud infrastructure differences | ❌ No | | Numeric precision | Inference engine variations | ❌ No | | Model snapshots | Version updates/changes | ❌ No |

Temperature and Sampling

Even with temperature=0.0 (greedy decoding):

Full determinism is NOT guaranteed
Minor variations can still occur due to infrastructure factors
Known bug: Claude CLI produces non-deterministic output for identical inputs

Achieving Maximum Consistency

To get the closest possible identical outputs between SDK and CLI:

import Anthropic from "@anthropic-ai/sdk";

const client = new Anthropic();

// Option 1: Use claude_code preset
const response = await client.messages.create({
  model: "claude-sonnet-4-20250514",
  max_tokens: 1024,
  // Match CLI system prompt as closely as possible
  system: "Your exact system prompt matching CLI",
  messages: [
    { role: "user", content: "What is the capital of Norway?" }
  ],
  // Use greedy decoding for maximum consistency
  temperature: 0
});

// Option 2: With Agent SDK query function
import { query } from "@anthropic-ai/agent-sdk";

for await (const message of query({
  prompt: "What is the capital of Norway?",
  options: {
    systemPrompt: {
      type: "preset",
      preset: "claude_code"
    },
    temperature: 0,
    model: "claude-sonnet-4-20250514",
    // Load project context like CLI does
    settingSources: ["project"]
  }
})) {
  // Process response
}

# Match the SDK configuration as closely as possible
claude -p "What is the capital of Norway?" \
  --model claude-sonnet-4-20250514 \
  --temperature 0

Still Not GuaranteedEven with perfectly matching configurations:

Output may differ between runs
Output may differ between SDK and CLI
No seed parameter exists to force reproducibility

Practical Implications

When to Use Each Interface

Use Case	Recommended Interface	Reason
Interactive development	Claude CLI	Full tool suite, project context
Programmatic integration	Agent SDK	Fine-grained control, embedding
Consistent API responses	Agent SDK + custom prompt	More control over system prompt
Batch processing	Agent SDK	Better for automation pipelines
One-off tasks	Claude CLI	Faster setup, immediate context

Design Recommendations

Don't rely on bit-perfect reproducibility

Build applications robust to minor output variations
Use structured outputs and validation

For production pipelines requiring consistency

Cache results when possible
Use structured outputs with JSON schema validation
Combine with deterministic logic and validation
Consider multiple generations with consensus

For matching CLI behavior in SDK

systemPrompt: {
  type: "preset",
  preset: "claude_code",
  append: "Your additional instructions"
},
settingSources: ["project", "user"]

System Prompt Token Impact

Configuration	Architecture	Notes
SDK (minimal)	Minimal default	Only essential tool instructions
SDK (claude_code preset)	Modular (~269+ base)	Matches CLI, varies by features
CLI (default)	Modular (~269+ base)	Additional context loaded conditionally
CLI (with MCP tools)	Modular + MCP	MCP tool descriptions add significant tokens

Note: Claude Code uses a modular architecture with 110+ system prompt strings. The base prompt is ~269 tokens, with individual components ranging from 18 to 2,610 tokens depending on features activated.Implication: The SDK’s minimal default gives you more context for your actual task, but at the cost of Claude Code’s full capabilities.

Summary

Q: What system prompts accompany the same message in SDK vs CLI?

The CLI uses a modular system prompt architecture with a ~269-token base prompt and 110+ conditionally-loaded components (tool instructions, coding guidelines, safety rules, project context). The SDK uses a minimal default with only essential tool instructions, though it can be configured to match CLI behavior using the claude_code preset.

Q: Is there a guarantee of identical output?

No. Even with matching system prompts, identical inputs, and temperature=0, there is no guarantee of identical outputs due to:

Absence of a seed parameter in Claude’s API
Floating-point arithmetic variations
Infrastructure-level non-determinism
Model architecture (Mixture-of-Experts) routing variations

Recommendation: Design systems to be robust to output variations rather than relying on deterministic behavior. For consistency-critical applications, use structured outputs, caching, and validation layers.

Technical Reports

Tips & Tricks

System Prompt Comparison

Claude CLI (Claude Code)

Claude Agent SDK

What Each Interface Sends

Example: “What is the capital of Norway?”

Customization Methods

Claude CLI Customization

Agent SDK Customization

Configuration Comparison

Output Consistency Guarantees

Factors Preventing Identical Output

Temperature and Sampling

Achieving Maximum Consistency

Practical Implications

When to Use Each Interface

Design Recommendations

System Prompt Token Impact

Summary

Sources

​System Prompt Comparison

​Claude CLI (Claude Code)

​Claude Agent SDK

​What Each Interface Sends

​Example: “What is the capital of Norway?”

​Customization Methods

​Claude CLI Customization

​Agent SDK Customization

​Configuration Comparison

​Output Consistency Guarantees

​Factors Preventing Identical Output

​Temperature and Sampling

​Achieving Maximum Consistency

​Practical Implications

​When to Use Each Interface

​Design Recommendations

​System Prompt Token Impact

​Summary

​Sources

System Prompt Comparison

Claude CLI (Claude Code)

Claude Agent SDK

What Each Interface Sends

Example: “What is the capital of Norway?”

Customization Methods

Claude CLI Customization

Agent SDK Customization

Configuration Comparison

Output Consistency Guarantees

Factors Preventing Identical Output

Temperature and Sampling

Achieving Maximum Consistency

Practical Implications

When to Use Each Interface

Design Recommendations

System Prompt Token Impact

Summary

Sources