Login

Instructions and System Prompts

Customize Quick Chat prompts and Agent Mode instructions with AGENTS.md.

A system prompt is a set of instructions you give the AI that shapes how it behaves in all conversations. Think of it as a persistent briefing: "You are an assistant that helps me with academic writing. Always cite sources. Respond in formal English."

Overview

Copilot has two instruction surfaces:

  1. Built-in system prompt — Internal Copilot behavior maintained by the plugin.
  2. User instructions — AGENTS.md for Agent Mode; selectable custom prompt files for Chat mode.

Built-In System Prompt

The built-in prompt is active by default and cannot be edited. It tells the AI:

  • It is "Obsidian Copilot" — an AI integrated into Obsidian
  • How to format Obsidian internal links: [[Note Title]]
  • How to format Obsidian image links: ![[image.png]]
  • How to format LaTeX math: use $...$ not \[...\]
  • How to handle @vault and @tool mentions
  • To use - for bullet points (not *)
  • To respond in the language of the user's query
  • To treat "note" as referring to an Obsidian note

This prompt ensures Copilot's output is correctly formatted for Obsidian and aware of its context.

You can disable it for a session from the chat settings. Doing so can break features such as Vault QA and memory, so leave it enabled unless you have a specific replacement.

Agent Mode Instructions

Agent Mode uses the standard AGENTS.md file:

  • Vault-wide instructions live at <vault>/AGENTS.md.
  • Project instructions live at <project>/AGENTS.md.
  • Project instructions are more specific and take precedence over vault instructions.

Each file has two edit surfaces, and both write the same file:

  • Vault instructions — Settings → Copilot → Basic → Custom instructions has a Custom vault instructions box that saves as you type. Open AGENTS.md beside it opens the file as an ordinary note instead.
  • Project instructions — the Edit Project dialog has a Project instructions box that saves when you accept the dialog. The project info popover's AGENTS.md row opens the file as a note.

Because these are ordinary notes, the box and the editor always agree; use whichever suits the edit. If a file is missing, opening or saving creates it. Copilot also adds an @AGENTS.md reference to the sibling CLAUDE.md without replacing other content, so Claude reads the same instructions as Codex and OpenCode.

Changes apply to new agent sessions.

Upgrading from an earlier version

  • A project that had a Project System Prompt is migrated automatically: the first time a session starts in it, that text moves into the project's AGENTS.md and is removed from the project record, so it lives in exactly one place.
  • The vault-level AGENTS.md starts blank. Your Chat system prompt files are not copied into it — they remain in the system-prompts/ sub-folder of your Copilot folder, and Settings shows a notice pointing there. Open one and paste across anything you want Agent Mode to keep following.

Your own hand-written AGENTS.md and CLAUDE.md files are never replaced.

Chat Mode Custom System Prompts

Chat mode custom system prompts let you add instructions on top of its built-in prompt.

Where They're Stored

Custom system prompts are stored as markdown files in your vault, in the system-prompts/ sub-folder of your Copilot folder:

copilot/system-prompts/

This location is derived from your Copilot folder. To move it, change the root in Settings → Copilot → Basic → Copilot folder location — every Copilot sub-folder follows that root, so it is no longer configured on its own. Changing the root affects only where new prompts are saved; existing prompt files stay where they are unless you move them yourself.

Creating a System Prompt

Create any .md file in the copilot/system-prompts/ folder, like any other note. Its filename (without .md) becomes the prompt's title, and the file body is the prompt. New files appear in the chat prompt picker automatically.

Writing Good System Prompts

Tips for effective system prompts:

  • Be specific: "Always respond in bullet points with no more than 5 bullets" is better than "be concise"
  • Set a persona: "You are an expert in cognitive science helping me build a Zettelkasten"
  • Define output format: Specify if you want headers, lists, prose, or code blocks
  • Set language: "Always respond in French" if you want non-English output
  • Limit scope: "Only answer questions related to my research notes on climate science"

Example system prompt:

You are a Zettelkasten assistant helping me build a knowledge base.
 
- Always connect new ideas to existing notes when possible
- Suggest up to 3 related concepts per response
- Format all note suggestions as [[Note Title]]
- Keep responses concise — under 200 words

Choosing a Prompt (Gear Icon)

Prompts are selected per conversation:

  1. Click the gear icon in the chat panel toolbar
  2. Select a system prompt from the list, or None (use built-in prompt)
  3. The selection applies to the current session and resets when you start a new chat

The Settings section that set a global chat default was removed. A default chosen in an earlier version keeps applying to new chats until you pick a different prompt (or None) in a conversation. This applies to Chat mode only — Agent Mode reads AGENTS.md instead.

How Prompts Combine

When you have a custom prompt active:

  1. The built-in Copilot prompt runs first
  2. Your custom prompt is appended after it

Both sets of instructions are active simultaneously. Your custom instructions can refine, restrict, or extend the default behavior, but they don't replace it.

Per-Project Instructions

Agent Mode projects use their own AGENTS.md. Legacy Chat mode projects retain their existing Project System Prompt field.

Related

ProjectsAgent Mode and tools