Build a Second Brain Claude Code Can Actually Use

The Obsidian + MCP setup that stops every new chat from starting at zero.

Every new Claude Code chat comes with the same tax:

What are we building?

What did we decide?

Where is the research?

What broke last time?

If you have to type that out every session, you are not using an agent.

You are renting a very smart blank page.

The fix: keep the memory in Obsidian, then give Claude Code controlled access to it through MCP.

Your notes stay yours. Claude just gets a way to search, read, and update them.

The idea

Your Obsidian vault becomes the place where your work lives.

Claude Code becomes the thing that can read it, search it, update it, and keep it organized.

Not just your notes.

Your active projects.

Your decisions.

Your research.

The loose threads you always forget to return to.

The trick is giving Claude access to the vault through MCP.

MCP is just the bridge that lets Claude Code use tools outside the chat.

In this case: your notes.

What you need

You need:

Obsidian

Claude Code

The free Local REST API with MCP plugin

Plugin:

https://github.com/coddingtonbear/obsidian-local-rest-api

Claude Code MCP docs:

https://code.claude.com/docs/en/mcp

1. Start with a clean vault

Do not connect Claude to ten years of random notes.

Make one vault for work that matters now:

00_inbox is where random thoughts, links, meeting notes, and screenshots go.

10_projects holds one folder per active project.

20_decisions is for choices you do not want to debate again next month.

30_research is for articles, transcripts, ideas, and useful references.

Simple wins here.

Your second brain does not need a beautiful taxonomy.

It needs a place where things can be found again.

Step 2: Give every project a context file

Inside each project folder, create a file named context.md.

Use this template:

This is the file Claude reads before it starts work.

It stops the cycle of:

“Here is the background…”

“No, not that project…”

“We already decided this last week…”

Step 3: Connect Claude Code to Obsidian

Install and enable the Local REST API with MCP plugin in Obsidian.

Open:

Settings → Local REST API

Copy the API key.

Then run this in your terminal:

Restart Claude Code.

Your first test should be boring:

If Claude can see them, the connection works.

Important: keep this server local.

Do not expose it to the public internet.

This MCP can read, create, edit, and delete notes. Treat the API key like a password.

Step 4: Use a closing ritual

The real value is not asking Claude random questions about your vault.

It is leaving every work session with better context than you started with.

At the end of a session, paste this:

That is it.

Five minutes of cleanup saves hours of recap later.

Step 5: Let your vault compound

Use this prompt at the beginning of a new session:

Use this prompt when you dump a pile of notes into your inbox:

Use this prompt once a week:

Now your AI is not just answering questions.

It is helping maintain the system you think with.

The mistake most people make

They connect an AI to their notes and immediately ask it to organize their entire life.

Bad move.

First, make it useful for one project.

Let it read the context.

Let it update the next actions.

Let it save one decision you would have otherwise forgotten.

Then repeat.

A second brain is not built by importing 10,000 notes.

It is built by making tomorrow’s work easier than today’s.

The point

The goal is not to build a perfect personal knowledge system.

The goal is to stop opening every new AI chat with a recap.

Your work should have memory.

Your decisions should have memory.

Your AI should have enough context to be useful before you start typing.

That is when a folder of notes becomes a second brain.

Bookmark this before you type “here’s the context again” one more time.

Follow @iiiichigo_chan

Prompts

Update the relevant context.md file.
 
Add any decisions we made.
Move useful notes out of 00_inbox.
List the next three actions.
 
Do not delete anything without asking.

Review everything in 00_inbox.
 
Group related notes.
Suggest where each item belongs.
 
Do not move or rename files until I approve the plan.

claude mcp add --transport http obsidian https://127.0.0.1:27124/mcp/ \
  --header "Authorization: Bearer <your-api-key>"

Review my active projects.
 
Flag stalled work.
Find decisions that are missing context.
Show me anything in 00_inbox that has been there for more than seven days.

00_inbox
10_projects
20_decisions
30_research
99_archive

List the folders in my Obsidian vault.
 
Do not change anything.

Read 10_projects/<project-name>/context.md.
 
Summarize the current status in five bullets.
 
Then ask me what changed since the last update.

# Project
 
## Goal
What are we trying to achieve?
 
## Current status
What is done? What is blocked?
 
## Decisions
What have we already chosen and why?
 
## Next actions
What should happen next?
 
## Important links
Docs, repos, people, files.

Links

• github.com/coddingtonbear/obsidian-local-rest-api
• code.claude.com/docs/en/mcp
• obsidian.md/