A second brain with Obsidian and Claude Code

Tools: Obsidian, Claude Code
Price: Obsidian free, Claude Code with a paid plan
Time: 30 min
Level: Terminal, beginner

A client asks what you agreed three months ago. The answer is somewhere: in a notebook, a phone note, an email to yourself. A “second brain” is one place where everything is written down. AI adds what was missing: sorting and searching, with no effort on your side.

Why this pair works

Obsidian stores each note as a text file in Markdown format, inside a folder it calls a vault. There is no closed database: just a normal folder that any program can read. Claude Code, Anthropic's assistant that works in the Terminal, reads and edits files in a folder. And Obsidian refreshes automatically when a file changes from outside: whatever Claude writes shows up in your notes straight away.

It suits a freelancer, a small business owner or a consultant who piles up meeting notes, ideas and decisions and wants to find them again without filing them by hand.

Set it up

Install Obsidian and create a vaultDownload Obsidian from obsidian.md, then create a vault, for example Documents/Second-brain.
Create a few simple foldersFor example inbox/ (everything that comes in, unsorted), clients/, projects/, journal/. No need for more: Claude will do the sorting.
Install Claude CodeOfficial command for Mac and Linux (Windows has its own command in the documentation):
Terminal
```
curl -fsSL https://claude.ai/install.sh | bash
```
Start Claude Code in the vaultIt asks you to sign in to your Claude account the first time.
Terminal
```
cd ~/Documents/Second-brain
claude
```

Give it the vault's rulesCreate a CLAUDE.md file at the root of the vault. Claude Code reads it at every session. The idea is explained in the tutorial A CLAUDE.md file for freelancers; here is a version for notes:

CLAUDE.md

# My second brain (Obsidian vault)

## Layout
- inbox/: unsorted notes, to be filed.
- clients/<name>.md: one note per client.
- projects/: one note per project.
- journal/YYYY-MM-DD.md: one note per day.

## Rules
- Answer in plain English.
- Link notes with Obsidian links [[Note name]].
- Never delete a note: move it to archive/.
- Do not rewrite my sentences: add, summarise or move.
- When you answer a question, cite the notes you used
  with their [[...]] link. If nothing answers it, say so.

Examples in a small business

Type your notes into inbox/ during the week (or dictate them), then ask Claude:

Prompt

Sort the notes in inbox/:
- anything about a client goes into their note clients/<name>.md
  (create it if it does not exist), under a dated heading;
- anything about a project goes into projects/;
- ideas with no follow-up go into ideas.md.
Add [[...]] links between the related notes.
Show me the list of moves before you make them.

And to find something again:

Prompt

What did I agree with [client] on price and deadlines?
Answer with the dates and links to the source notes.

On Friday, one last prompt such as “Summarise my week from journal/ and list the actions not done” gives you a weekly review without copying anything.

Useful settings

Links: by default Obsidian creates [[Note name]] links. Keep that format in your CLAUDE.md so Claude writes the same ones.
Private folder: to stop Claude Code's file-reading tools from opening a folder, add a deny rule in .claude/settings.json at the root of the vault:
.claude/settings.json
```
{
  "permissions": {
    "deny": ["Read(./private/**)"]
  }
}
```
Approvals: by default, Claude Code asks for your approval before editing a file. Keep it that way until you know its habits well.

Limits and cost

Obsidian is free with no limits, including for work; a commercial licence exists (US$50 per user per year) but it is optional. Official sync between devices is paid (from US$4 a month).
Claude Code requires a Claude Pro, Max, Team or Enterprise plan, or a Console account billed per use.
Claude reads your notes when you ask the question: with thousands of notes, a clear structure (folders, file names) helps it find things fast.

Ground rules. The notes Claude reads are sent to Anthropic to be processed: keep passwords, access codes, health or banking data out of this vault. The curl … | bash install command runs a downloaded script: only copy it from Anthropic's official documentation. Before letting Claude sort anything, back up the vault (a copy of the folder, Time Machine or Git).

Sources

Want a second brain for your whole team, connected to your email and CRM? That is the kind of automation I set up.