Your Journey to an AI-Enhanced Second Brain

This guide will walk you through setting up the Claude Code + Obsidian workflow that powers the Claudsidian system.

What You’ll Need

Before you begin, make sure you have:

  • Obsidian installed
  • Claude Code CLI installed
  • A Claude API account (or Claude Code subscription)
  • Basic familiarity with markdown and note-taking

Step 1: Configure Your Obsidian Vault

First, set up your Obsidian vault for optimal AI integration:

  1. Create a dedicated vault (or use an existing one)
  2. Organize your folder structure:
    MyVault/
├── PROJECTS/         # Active projects
├── AREAS/            # Areas of responsibility
├── RESOURCES/        # Reference materials
└── ARCHIVES/         # Completed items
  3. Enable core plugins: Templates, Daily notes, Backlinks

Step 2: Install and Configure Claude Code

Install the Claude Code CLI and set it up to work with your vault:

# Install Claude Code (if you haven't already)
# Follow instructions at: https://docs.anthropic.com/claude/docs/claude-code

# Navigate to your Obsidian vault
cd /path/to/your/ObsidianVault

# Initialize Claude Code
claude init

Step 3: Set Your Working Directory

The key to the Claudsidian workflow is setting Claude Code’s working directory to your Obsidian vault:

# Always work from your vault directory
cd /path/to/your/ObsidianVault

# Or set it in your shell profile
export CLAUDE_WORKSPACE="/path/to/your/ObsidianVault"

Step 4: Create Your First AI-Enhanced Note

Try this workflow:

  1. Start Claude Code in your vault directory
  2. Ask Claude to help with a task or project
  3. Have Claude create notes documenting the conversation
  4. Review and edit the notes in Obsidian
  5. Link notes together to build your knowledge graph

Example prompt:

I'm working on a new web project. Help me brainstorm the architecture
and create a project note in PROJECTS/ documenting our discussion.

Step 5: Develop Your Workflow

Here are some powerful workflows to explore:

Project Planning

Ask Claude to help you break down complex projects and create structured notes with tasks, decisions, and timelines.

Research Synthesis

Have Claude help you synthesize information from multiple sources and create connected notes in your vault.

Daily Notes Enhancement

Use Claude to help review your daily notes and extract important insights into permanent notes.

Code Documentation

When working on code projects, have Claude document your decisions and create technical notes in your vault.

Best Practices

  1. Be explicit about file locations: Tell Claude exactly where to create or update files
  2. Review everything: Claude is helpful but you’re the curator of your second brain
  3. Link liberally: Create connections between notes using [[WikiLinks]]
  4. Use templates: Create note templates for common workflows
  5. Keep conversations focused: One topic per conversation makes better notes

Next Steps

Now that you have the basics:

  • Explore the Blog for workflow tips and examples
  • Experiment with different types of notes and projects
  • Build your knowledge graph over time
  • Share what you learn with the community

Need Help?

Having trouble getting started? Check out our blog posts or reach out to the community.

Remember: Your second brain is personal. Adapt this system to match your thinking and working style.