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How to set up your AI brain in Obsidian (and why it beats Notion, Google Drive and files on your computer)

by Samantha 16 September 20269 min read

When I first started using AI properly in my business, my business was spread across Google Docs, a Notion workspace, a folder of downloads and my own head. Every time I wanted Claude to help with a client, I'd go looking for the right document, copy it, paste it into the chat and explain the rest from memory.

It worked, but only for that one chat. The next day I'd do it all again, and anything I'd decided the day before was gone unless I remembered to paste that in too.

Now everything lives in one folder on my computer, written in Obsidian. Claude reads it before it does anything. My other AI assistant reads the same folder. My AI employees read it when they pick up a task. I update a document once and every one of them knows.

That folder is my AI brain, and this post is how to build yours.

What you'll have at the end

One Obsidian vault, which is just a folder on your computer, set up like this.

My Business Vault/
├── 00 Knowledge Base/        → the truth: finished, current documents only
│   ├── Identity/             → who you are, your brand, how you write
│   ├── Vision & Goals/       → where the business is going
│   ├── Business/             → your offers, prices & how you deliver
│   ├── Clients/
│   │   └── Client A/         → profile, scope, STATUS, daily logs
│   ├── Content/              → strategy, pillars & published posts
│   └── Systems/              → your processes & how your tools are set up
├── 01 My Workspace/          → your own work in progress
├── 02 Claude's Workspace/    → everything Claude drafts, before you approve it
├── 03 Skills/                → the job description for each AI employee
├── 04 Archive/               → old versions, so nothing gets deleted
└── CLAUDE.md                 → the instructions Claude reads first

This is a simplified version of mine. The rule mine runs on is one line: tasks live in your task manager, knowledge lives in the vault. A task doesn't go in the vault. The output of doing it does.

Why Obsidian, and not Notion, Google Drive or files on your computer

I've used all four. Here's why the brain ended up in Obsidian.

AI reads Markdown best, and Obsidian saves everything as Markdown. Markdown is a plain text file with simple formatting, and you'll see it as .md. You write in Obsidian like a normal document, and behind the scenes every note is saved as an .md file in a normal folder. There's nothing to convert and nothing to export.

Google Drive makes you convert everything first. I live in Google Workspace, and a Google Doc is not an .md file. Every document I wanted Claude to read had to be converted and downloaded first, and when I changed the Google Doc, the copy Claude had was out of date. You can keep your vault inside Google Drive to back it up, but anything that starts life as a Google Doc still has that friction, which is why I write my documents in Obsidian in the first place.

Notion keeps your business inside Notion. Your pages live in Notion's workspace rather than in a folder you own, so Claude has to go through Notion to read them, one page at a time, instead of opening a folder. When the whole brain is a folder on your computer, Claude can read all of it, search it and write back into it in the same chat.

Files on your computer are close, but they're not built for writing in. A folder of Word documents and PDFs is on your computer, but Claude reads them less well, and you won't want to write and update your documents in a file browser. Obsidian gives you the folder and a nice place to write in it.

It isn't tied to one AI. Because the vault is just a folder of text files, anything can read it. Atlas, my second AI assistant, runs off the exact same vault. If a better tool comes along next year, the brain comes with me.

Obsidian is free. The one paid add-on I use is Obsidian Sync, which keeps the vault up to date across my devices.

What you need before you start

  • Your AI org chart, if you've done it. It tells you which AI employees you'll build, so you know what they'll need to read. If you haven't, it's step 1: How to create your AI org chart before you build any AI employees.
  • The Claude desktop app on a paid plan, with the Claude Code tab.
  • Your key documents to hand: your offers and prices, your about-me, your brand notes, and your notes for one client.

You don't need to know how to code, and you don't need to move your whole business in on day one. One client is enough to start.

Step 1 - Create the vault

  1. Go to obsidian.md and download Obsidian for your computer.
  2. Open it and click Create new vault.
  3. Give it a name, like "My Business Vault".
  4. Choose where it's saved. Pick somewhere you'll find again, like your Documents folder.
  5. Click Create.

You'll see an empty Obsidian window with your vault's name at the top left. That's your AI brain, and right now it's an empty folder.

Step 2 - Let Claude build the structure

Open the Claude desktop app, click the Claude Code tab and start a new chat. Click the + at the bottom of the chat and choose your vault folder.

Then paste this.

This folder is my new AI brain. It's an Obsidian vault & I want every AI
I use to read my business from here.

Create this folder structure for me:
00 Knowledge Base (with Identity, Vision & Goals, Business, Clients,
Content & Systems inside), 01 My Workspace, 02 Claude's Workspace,
03 Skills & 04 Archive.

Put a short README.md in each folder saying what goes in it, in one or
two sentences. Show me the structure before you create anything.

Claude will show you the folders and ask if they're right. Change anything that doesn't fit your business, then tell it to go ahead.

Go back to Obsidian and you'll see every folder in the left-hand sidebar.

Step 3 - Move your business in

This is where the brain gets its knowledge.

Now I want to move my business into the vault. I'm going to give you my
documents one at a time. For each one, turn it into a clean .md file,
put it in the right folder & tell me where you put it.

Start by asking me for my offers & prices. Then my about-me & brand
notes. Then everything I have for one client.

If something I give you is out of date or contradicts another document,
ask me which one is true rather than guessing.

You can paste text straight into the chat, or drag a file in. If your documents are Google Docs, tell Claude and it will walk you through getting them out.

What you'll see is your vault filling up in Obsidian as Claude works. Open each file as it lands and read it. If Claude has written something about your business that isn't true, fix it now, because every AI that reads this later will believe it.

If you want to know exactly what goes in each document and how to structure it, I wrote that up separately: The 6 documents every freelancer should have in their AI brain.

Step 4 - Write the instructions Claude reads first

The folders tell Claude what you know. The CLAUDE.md file tells it how to use them. Claude reads it at the start of every chat in this folder, so it's where your rules go.

Now write a CLAUDE.md file in the top of my vault. It should tell you:
- who I am & what my business does, in a few lines
- what each folder is for & where to look first
- that 00 Knowledge Base is the truth & only holds finished, current
  documents
- that anything you draft goes in 02 Claude's Workspace until I approve it
- that old versions go to 04 Archive & nothing gets deleted
- that passwords & keys never go anywhere in the vault

Interview me for anything you don't know. Show me before you save.

Keep it short. Mine is a pointer that tells Claude who I am and where the real documents live, so it can read the detail when a task needs it rather than all at once.

Step 5 - Test it

Start a brand new chat in the Claude Code tab and attach the vault folder again. Then ask it something only your business would know.

Read my AI brain. Then tell me what I sell, who my client is & what's
going on with them right now. Tell me which files you read to answer.

If the answer is right and it names your files, the brain works. If it's vague or wrong, look at the files it read. The fix is almost always in the document, not the prompt.

The catch, and the fix

The catch is that a brain goes out of date the day after you build it. A client call moves a project on, a decision gets made in a chat and never written down, and three weeks later Claude is confidently telling you about something that stopped being true a fortnight ago.

The fix is to never rely on remembering. When you decide something important in a chat, tell Claude to save it into the vault before you close it. Then, when you're ready, hand the updating to an AI employee. Mine reads every chat, every ClickUp task and every file I changed that day, and writes it into each client's log and status page every night: The AI employee that updates my AI brain every night.

The second catch is that the vault lives on your computer. Claude can read it when you're working on that computer, and your AI employees can read it while that computer is on. If you want the same brain on your other devices, that's what Obsidian Sync is for.

What this looks like as a business

Every business owner you support is trying to get AI to understand their business, and most of them are doing it by pasting documents into chats. Setting up one vault that holds the truth about their business, and every AI they use reads from, is the foundation every other AI build sits on. You're paid for knowing what to build and in what order, and the brain comes before any employee.

Start with one

Create the vault this week and move in three things: your offers and prices, your about-me and one client. Then run the test in Step 5.

Once the brain is set up, the next step is where the work lives. My AI employees get their tasks from ClickUp and read the vault to do them, and that's how the whole team fits together: How I Built an AI Team in Claude.

If you haven't got your AI brain set up, that's the foundation for all of this: start here.

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