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← All writingPublished October 20, 2026

How to build a second brain with Claude Cowork and Obsidian

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To build a second brain with Claude Cowork and Obsidian, move every note you have into one Obsidian vault, sort it by whose words each note holds and what stage it's at, then select the vault's folder in Cowork and give it folder instructions. New notes land in an inbox, and Cowork files them with a prompt that moves nothing until you approve.

Most guides start from an empty vault and a terminal. Most people start from years of notes spread across Bear, Notion, Evernote and Apple Notes, and would rather never open a terminal at all. So this one starts with the notes you already have, in the order I build one.

How Claude and Obsidian work together#

Obsidian keeps notes as plain Markdown files in a folder on your computer, which it calls a vault. Nothing is locked inside the app, so anything that reads text can read your notes, Claude included.

Cowork is the part of the Claude desktop app that works on the files on your computer, on Mac and Windows, on any paid plan. It reads and writes only the folders you connect, so connecting your vault is all it takes for Claude to work on your notes, with no plugin and no connector in between. Obsidian and Claude never talk to each other directly. They share the folder.

Get every note out first#

Obsidian's Importer plugin brings notes in from Notion, Evernote, Apple Notes, Bear, Google Keep, OneNote and ten more apps and formats. Before you run it, check that each export is whole. Notion's Markdown and CSV export leaves out the pages nested inside other pages unless Include subpages is switched on, and then every link to a nested page points at nothing. Count the notes in each app and in each export, and don't move on until the numbers match.

Keep the original exports untouched in a folder of their own. Everything after this step changes files, and you want to be able to check any note against where it came from.

When a New York Times bestselling author asked me to move her notes into Obsidian, she thought she had a few, mostly in Bear. With Notion's subpages included, they came to more than 18 GB, sixteen years of notes from Bear, Evernote and Notion. Bear's titles were whole sentences, and most Windows apps can't open a file path longer than 260 characters, so a straight copy would have broken. The count is where you find out what you're really moving.

Decide the folders with two questions#

Folders work best when they answer questions whose answers never change. Two fit almost anyone. Whose words does this note hold, yours or someone else's? And what stage is it at, a loose thought or part of a project?

00 Inbox        everything new lands here
01 Notebook     your own thoughts, not tied to a project yet
02 Projects     your own work, one folder per project
03 Archive      other people's words, clippings and PDFs
09 System       templates and dashboards

Topics go in tags, because a note can be about five things and sit in only one folder. Obsidian's tags can nest, such as #theme/travel, and they can live in the tags property at the top of a note, where Claude can read and add them without touching your text.

Properties are the small block of fields at the top of a note, and they're where a vault keeps its order. Give each kind of note a template with its own properties, such as a source note with its author and where it came from. Obsidian's Templates core plugin drops one into a new note, and Claude can fill the same fields when it files something, so every note of a kind can be sorted and found the same way.

Link with a reason. A graph where everything links to everything looks busy and tells you very little. Keep one hub note per subject that lists its notes with a line on why each belongs, and Obsidian's backlinks then show that hub inside every note it names.

Keep anything private in a vault of its own, in a folder you never connect. Cowork can only reach the folders you connect, so those notes stay out of its reach whatever the instructions say.

Connect the vault to Cowork#

Open Cowork in the Claude desktop app and select your vault's folder. Folder instructions give Claude standing context whenever it works in that folder, the way a short briefing would for a new assistant. A few clear rules do most of the work.

# My vault

This is my second brain in Obsidian. Every note is a Markdown file.

- 01 Notebook and 02 Projects hold my own words. 03 Archive holds other people's.
- Never change the text of a note. You may add properties, rename a file and move it, once I approve.
- Topics go in the tags property, as nested tags such as theme/travel.
- Never delete a file.
- When you can't tell whether I wrote a note or saved it, ask me.

While you're setting up, run Cowork in Manual mode, where it asks you to approve each action. In every mode, it asks before it permanently deletes a file.

If you'd rather use Claude Code#

Claude Code does the same work from a terminal. It reads a file called CLAUDE.md from the folder it starts in, at the start of every session, so start it in your vault and put the same instructions in that file. Running /init writes a first draft, and Anthropic suggests keeping the file under 200 lines. Both tools read the same files, so you can switch later without changing the vault.

An inbox Claude sorts, and you approve#

Everything new goes into 00 Inbox, whether it's a thought from your phone, a clipped article or a PDF. Once a week, run a triage prompt.

Read every note in 00 Inbox. Show me a table with each file, the folder it should go to,
the tags it should get and why. Move nothing until I approve.
If you can't tell whether I wrote a note or saved it, ask me,
and add my answer to the folder instructions.

That last line is what makes the vault better over time. Claude can update its folder instructions during a session, so each answer becomes a rule, and it asks less every week.

To see what's waiting, make an Inbox view with Bases, the core plugin that shows your notes as a table you can sort and filter by their properties.

Ask it what you know#

This is the part people build a second brain for. Ask Claude how many notes you have on a subject and what they say, which of your loose thoughts belong to a project you're working on, or what you wrote about something years ago. Ask it to name the notes it drew on, so you can open them and check.

Start with a subject you know well. If the answer matches what you remember writing, you can trust it on the subjects you don't, and if it misses something, the miss usually points at a note in the wrong folder or without a tag, which is a quick fix in the instructions.

Keep your words yours. When you want a draft from your notes, ask Claude to quote and point rather than rewrite, and the voice in the draft stays the one in the notes.

Plain files make all of this safe to try. If you stop using Claude tomorrow, the vault is still a folder of your own notes that opens in any editor.

That's the vault I built for that author, sorted by whose words a note holds so her own thoughts can grow into her next book, and on the night it arrived she wrote back, "Hurrah! It works!" If you'd rather have yours built, tell me where your notes live.

Sources#