A complete setup tutorial. Written September 2026, checked against the current Claude Code docs.

Why this combo

Your brain is good at having ideas.

It is terrible at storing them.

You think of a million things through the day, then sit down to work and they're gone. A second brain fixes the storage problem. Obsidian stores the info, Claude helps you find and use what you need.

The reason this specific pairing works is boring and important: Obsidian saves everything as plain Markdown files on your own computer. No database, no export lock-in. And Claude Code is a terminal agent that reads and writes plain files. Point it at your vault and it can search your notes, connect them, draft from them, and file new stuff for you.

You own the files. The AI is a layer on top. If you stop paying for Claude tomorrow, your notes are still sitting there as text files.

Setup takes about 2 hours, start to finish.

Step 1: Install Obsidian and create a vault

1. Download Obsidian from obsidian.md. It's free.
2. Create a new vault. A vault is just a folder on your computer where every note lives.
3. Put it somewhere easy to reach from a terminal, like ~/Documents/SecondBrain. Avoid burying it 6 folders deep.

Step 2: Set up the terminal

Claude Code runs in a terminal, and the cleanest setup is a terminal pane inside Obsidian itself. Claude works on one side while your notes update live on the other.

First, the terminal pane:

1. Open Obsidian Settings → Community plugins
2. Click Turn on community plugins (Obsidian ships with them off, this is normal)
3. Click Browse and search for Terminal (the one by polyipseity)
4. Install it, then hit Enable
5. Open the command palette (Cmd+P on Mac, Ctrl+P on Windows) and run Terminal: Open: Integrated terminal (current)