How to build a second brain in Markdown, step by step

To build a second brain in Markdown, keep every note as a plain file in one folder, and run a loop of five steps: capture, organize, link, retrieve and review. This guide uses Loam, our free, open source notes app for Mac, to show a real vault layout and the commands for each step. The method works in any app that opens a folder of Markdown files.

What is a second brain?

A second brain is a trusted place outside your head where you keep what you learn, so you can find it and use it later. The term comes from the book "Building a Second Brain" by Tiago Forte.

The book offers two ideas. PARA sorts information by how actionable it is: Projects, Areas, Resources and Archive. CODE describes the work you do with that information: Capture, Organize, Distill and Express. This guide borrows from both in general terms and applies them to a folder of files. The book remains the place for the full method.

The loop below is the one we follow. Notes enter by capture, get a place when you organize them, gain connections when you link them, and come back when you retrieve them. Review keeps the loop honest.

Sources: Building a Second Brain: official site ↗

What does a second brain vault look like?

A vault is a folder. Here is a layout for a second brain. Inbox/, Daily/, Projects/, Habits/, Attachments/ and .loam/ follow Loam's conventions. Areas/, Resources/ and Archive/ are plain folders that follow PARA, and you can name them as you like.

Notes/
├── Inbox/                         unsorted captures; new boards and drawings land here
├── Daily/
│   └── 2026-11-03.md              one note per day, opened with Cmd+D
├── Projects/
│   └── Website redesign/
│       ├── Website redesign.md    the project note
│       └── Write homepage copy.md  a task note
├── Areas/
│   └── Health/
│       └── Running.md
├── Resources/
│   └── Reading/
│       └── Reading.base           a collection over the notes of the folder
├── Archive/
├── Habits/
│   └── Meditate.md
├── Attachments/                   images and PDFs pasted into notes
├── .loam/
│   ├── config.json                plugin settings and shortcuts
│   └── templates/daily.md         the daily note template
└── .trash/                        deleted notes, kept for 30 days

Loam writes its own files in the hidden .loam/ folder and leaves every note where you put it. Your first vault explains what Loam creates in a new vault.

Step 1: capture notes fast

Capture first and sort later. The goal is to get an idea out of your head in seconds, without deciding where it belongs. Loam gives you three ways in.

• Press Cmd+D to open today's daily note and write there. It is one Markdown note per day, such as Daily/2026-11-03.md.
• Press Cmd+N for a new note, and create it in Inbox/ from the Files panel.
• From a terminal, add a line to today's note with daily.append.

loam --vault ~/Notes daily.append text="Idea: do a weekly review on Friday"

A template gives every day the same start. Loam reads it from .loam/templates/daily.md, and {{date}} becomes the day. Tasks written in any note, such as - [ ] Call Bob due:2026-11-10, gather in one task list, and the quick add box writes a task to today's note.

# {{date}}

## Plan
-

Step 2: organize notes by use

Organize by what a note is for. Its topic comes second. That is the PARA idea: a project has an end, an area is a duty you keep up, a resource is something you may need later, and the archive holds what is finished.

Folders say where a note belongs. Properties say what state it is in. They are key: value lines in YAML between two --- lines at the top of a note:

---
status: doing
created: 2026-10-28
tags: [project, work]
---

# Plan

To sort an inbox note, move it and set a property. notes.rename moves the note and rewrites the links that point to it, and query.set-property changes one property without touching the rest of the note.

loam --vault ~/Notes notes.rename from=Inbox/Idea.md to=Resources/Reading/Idea.md
loam --vault ~/Notes query.set-property path=Resources/Reading/Idea.md key=status value=read

Step 3: link notes together

Links turn a pile of notes into a network. In Loam a link is a standard Markdown link, with a path relative to the note that holds it. From Daily/2026-11-03.md, a link to a run log looks like this: [Running](../Areas/Health/Running.md). Loam uses these links for backlinks, the graph and renames.

• Backlinks are the notes that link to the open note. The Links tab of the right sidebar lists them with the line where they link, and it also lists unlinked mentions of the note name.
• Tags are words such as #project or #work/q4 in the text, or an entry in a tags: property. The Tags section of the left sidebar lists each tag with its count.
• The command line gives you the same answers: notes.backlinks prints the notes that link to a note, and query.run finds the notes with a tag.

loam --vault ~/Notes notes.backlinks path=Areas/Health/Running.md
loam --vault ~/Notes query.run tag=project

One catch: wikilinks such as [[Plan]] are styled in the editor, but they do not count for backlinks, the graph or renames. Use a standard Markdown link whenever a link must be tracked. Link while you write. A note with no links is hard to find again. See Links, backlinks and search for the details.

Step 4: retrieve notes by name, text or meaning

Loam finds notes in three ways: by file name, by the text inside them, and by what they mean. Name and text search work out of the box. Search by meaning needs Truffle, a separate tool.

In the app, Cmd+O opens the quick switcher and Shift+Cmd+F opens a search popup. To turn on search by meaning, install Truffle with brew install azilone/tap/truffle, then run truffle setup or start truffle serve.

An AI agent searches the same way. It runs loam search.content q=roadmap on the vault and reads the lines that match. See Agents and how to use Claude Code with your notes.

Step 5: review every week

Review is what keeps a second brain from filling up with notes you never read again. Set aside a short slot once a week, and work through this list.

• Empty Inbox/: move each note to a project, an area or a resource, or send it to the trash with files.trash, which keeps it in .trash/ for 30 days.
• Open the task list. Today shows overdue tasks and those due today, Upcoming lists the rest by date, and Inbox shows open tasks without a date.
• Check your projects. projects.list status=Active shows each project with its task counts and an overdue flag.
• Open your collections. A collection shows a folder of notes as a table, a kanban board or a gallery, based on their properties.
• Archive what is finished: mark the project Done and move its notes to Archive/.

loam --vault ~/Notes tasks.list done=false
loam --vault ~/Notes projects.list status=Active
loam --vault ~/Notes collection.entries path=Resources/Reading/Reading.base

How do you distill and express what you saved?

Distill means cutting a note down to the few lines you would want to read again. Express means using your notes to make something: an article, a talk, a decision. Files make both easy to keep honest.

• For distilling, add a short summary at the top of a long note, in your own words, and keep the rest below it.
• For expressing, draft in a note of its own and link to the notes it draws on. Each source note then lists the draft in its backlinks.
• For planning, a board lays notes out on a whiteboard as cards joined by arrows. A card that shows a note stores only its path, so the note stays one note.

Create a board with canvas.new folder=Boards title=Talk, or from the app. Boards are JSON Canvas files, and Obsidian reads them too. See Boards.

Why do plain files keep a second brain alive?

A second brain only works if you can keep using it for years. Plain files outlast apps. A text file written in the 1990s still opens today in any editor, and a Markdown note needs no account, no server and no subscription to stay readable.

Tools come and go. When your notes are a folder, changing tools means opening the same folder in another app. Loam keeps to open formats for that reason: CommonMark and GitHub Flavored Markdown for notes, YAML for properties, .base files for collections, JSON Canvas for boards and Excalidraw for drawings. Read more in why Markdown is still the right format and where your notes live.

What are the limits of this setup?

• Loam runs on macOS 26 or later, on Apple silicon, and has no iPhone or Android app.
• It is single user. You can share a vault through Git.
• It has no web clipper, so capture away from your Mac needs another tool whose notes you paste into Inbox/.
• Its plugin catalog is younger and smaller than Obsidian's.

The method itself does not depend on Loam. If you use Obsidian, the same steps work in your vault, and Loam opens an Obsidian vault as it is. See Loam vs Obsidian.

Sources: Loam docs: Write and organize notes ↗ · Loam docs: Links, backlinks and search ↗ · Loam docs: Daily notes ↗

Try Loam

Loam is free and open source. Install it with one command, open a new folder as a vault, and press Cmd+D to write your first daily note. If you want to see how it differs from other apps, read Loam vs Obsidian or browse every comparison. To go one step further, try Zettelkasten in Markdown.