System Prompt Override (GEMINI_SYSTEM_MD)

The core system instructions that guide Gemini CLI can be completely replaced with your own Markdown file. This feature is controlled via the GEMINI_SYSTEM_MD environment variable.

Overview

The GEMINI_SYSTEM_MD variable instructs the CLI to use an external Markdown file for its system prompt, completely overriding the built-in default. This is a full replacement, not a merge. If you use a custom file, none of the original core instructions will apply unless you include them yourself.

This feature is intended for advanced users who need to enforce strict, project-specific behavior or create a customized persona.

Tip

You can export the current default system prompt to a file first, review it, and then selectively modify or replace it (see “Export the default prompt”).

How to enable

You can set the environment variable temporarily in your shell, or persist it via a .gemini/.env file. See Persisting Environment Variables.

• Use the project default path (.gemini/system.md):

  • GEMINI_SYSTEM_MD=true or GEMINI_SYSTEM_MD=1
  • The CLI reads ./.gemini/system.md (relative to your current project directory).

• Use a custom file path:

  • GEMINI_SYSTEM_MD=/absolute/path/to/my-system.md
  • Relative paths are supported and resolved from the current working directory.
  • Tilde expansion is supported (e.g., ~/my-system.md).

• Disable the override (use built‑in prompt):

  • GEMINI_SYSTEM_MD=false or GEMINI_SYSTEM_MD=0 or unset the variable.

If the override is enabled but the target file does not exist, the CLI will error with: missing system prompt file '<path>'.

Quick examples

• One‑off session using a project file:
  • GEMINI_SYSTEM_MD=1 gemini
• Persist for a project using .gemini/.env:
  • Create .gemini/system.md, then add to .gemini/.env:
    • GEMINI_SYSTEM_MD=1
• Use a custom file under your home directory:
  • GEMINI_SYSTEM_MD=~/prompts/SYSTEM.md gemini

UI indicator

When GEMINI_SYSTEM_MD is active, the CLI shows a |⌐■_■| indicator in the UI to signal custom system‑prompt mode.

Variable Substitution

When using a custom system prompt file, you can use the following variables to dynamically include built-in content:

• ${AgentSkills}: Injects a complete section (including header) of all available agent skills.

• ${SubAgents}: Injects a complete section (including header) of available sub-agents.

• ${AvailableTools}: Injects a bulleted list of all currently enabled tool names.

• Tool Name Variables: Injects the actual name of a tool using the pattern: ${toolName}_ToolName (e.g., ${write_file_ToolName}, ${run_shell_command_ToolName}).

  This pattern is generated dynamically for all available tools.

Example

# Custom System Prompt

You are a helpful assistant. ${AgentSkills}
${SubAgents}

## Tooling

The following tools are available to you: ${AvailableTools}

You can use ${write_file_ToolName} to save logs.

Export the default prompt (recommended)

Before overriding, export the current default prompt so you can review required safety and workflow rules.

• Write the built‑in prompt to the project default path:
  • GEMINI_WRITE_SYSTEM_MD=1 gemini
• Or write to a custom path:
  • GEMINI_WRITE_SYSTEM_MD=~/prompts/DEFAULT_SYSTEM.md gemini

This creates the file and writes the current built‑in system prompt to it.

Best practices: SYSTEM.md vs GEMINI.md

• SYSTEM.md (firmware):
  • Non‑negotiable operational rules: safety, tool‑use protocols, approvals, and mechanics that keep the CLI reliable.
  • Stable across tasks and projects (or per project when needed).
• GEMINI.md (strategy):
  • Persona, goals, methodologies, and project/domain context.
  • Evolves per task; relies on SYSTEM.md for safe execution.

Keep SYSTEM.md minimal but complete for safety and tool operation. Keep GEMINI.md focused on high‑level guidance and project specifics.

Troubleshooting

• Error: missing system prompt file '…'
  • Ensure the referenced path exists and is readable.
  • For GEMINI_SYSTEM_MD=1|true, create ./.gemini/system.md in your project.
• Override not taking effect
  • Confirm the variable is loaded (use .gemini/.env or export in your shell).
  • Paths are resolved from the current working directory; try an absolute path.
• Restore defaults
  • Unset GEMINI_SYSTEM_MD or set it to 0/false.