Building a Second Brain in Obsidian

Have you ever thought about how much information you consume every week?

You read books, articles, tweets, watch documentaries — all of these are a goldmine of ideas.

But what are you doing with it? How much of it is leading to something useful? It's tempting to believe that you'll remember it and use those ideas in your next project, but that's very optimistic. And wrong.

In reality, we read something and we forget about it 2 days later. And if we remember it, our memory of it starts to distort the more time goes on.

You simply can't remember everything you come across. That's why it's important to have a structure in place that can relieve you of the burden of keeping track of your knowledge. A second brain, if you will.

What's a second brain, anyway?

"Building a second brain" is a phrase coined by Tiago Forte and it's all about building a system where you can collect, refine, and process ideas that you come across or generate throughout the week.

Instead of just remembering the cool idea you read in a blog post, you put it in your second brain and you link it to other ideas that you have. Do this enough, and you get a web of notes that lead to epiphanies and new insights.

Build a second brain

When I first heard about it I was skeptical. It sounded a bit woo-woo, a lot of the work is upfront, and there was no guaranteed payoff. But after having a couple of "oh snap!" moments I think it's one of the most valuable things I have ever done.

The main benefit of a second brain is that it optimizes your thoughts for serendipity or unexpected insights.

A big part of having breakthrough ideas is stumbling across information you didn't think you needed. This isn't possible with search engines. They can only provide you with information you think you need. A second brain gives you information you didn't know you needed.

The tools you need

Tools are to productivity nerds what catnip is to cats. There's a new note-taking app coming out every day and everyone's constantly jumping ship. To build a second brain, however, you only need a few tools.

Obsidian is the main tool I use to build a second brain. It has a nice balance between the right features and the flexibility to work how you want. The most important feature is that it allows you to easily create connections between notes.

Obsidian md

Copy and pasting paragraphs and ideas you've read isn't ideal if you do it multiple times a day. Liner solves this problem. You can use it to highlight, annotate, and extract passages from articles and PDFs. You can then export your highlights to text, Evernote, and more.

If I read interesting articles the moment I came across them I wouldn't be able to get any work done. Instead, I just save them to pocket. It acts as a holding area for articles I want to read or videos I want to watch. Every week, I set aside some time to go through it and process it.

Evernote (optional)
I don't use Evernote too often. It does, however, have a good browser extension for information capture. LINER doesn't work with tweets and can't save images, for example, so I use Evernote to pick up the slack.

I only use it for information capture though and I regularly move my notes from Evernote into Obsidian.

Obsidian works with markdown files stored on your local machine. I find this easier to work with, but it does come with the downside of not being able to sync your second brain on different computers.

To solve this, I put my second brain in a folder in Dropbox. This allows me to work on my second brain from multiple computers and still have everything up to date.


Roam research
Roam is the biggest and most well-known alternative to Obsidian, so much that Obsidian is more of an alternative to Roam than the other way around.

There are two big differences between the two:

  • Roam is cloud-based, Obsidian uses local markdown files
  • Every paragraph in Roam can be referenced on another page. This isn't possible with Obsidian.

That last point requires some more explaining. In Roam, you can create an entire article without writing a single word. You simply create a new page and start referencing paragraphs from other notes.

In Obsidian, this isn't possible. Well, not entirely. You can embed other notes and narrow it down to a specific heading, but it requires you to create the note in such a way that it can be referenced easier.

Whether Roam or Obsidian is for you depends on what you value the most. Do you value the productivity part? Go for Roam. Value the privacy and personal knowledge management side of it? Use Obsidian.

How do you structure your second brain?

Short answer: as little as possible.

With other note-taking systems, you're add everything to the right category and give them proper tags. This is good if you want to create a catalog of something, but it prevents you from stumbling on ideas you didn't know you needed.

With this system, you throw everything onto a pile and let it sit there with all the other notes. The beauty is in its chaos.

Think of it this way: Instead of a system you need to assemble, think of it as something organic that you need to cultivate. You need fertile ground for ideas to grow, and in this case, that fertile ground is your collection of notes. Again, the biggest reason you're putting all your notes together is it allows you to see connections that otherwise wouldn't be possible.

That said, you do want some structure in your notes.

Personally, I only have 4 main folders:

|-- 0.Attachments
|-- 1.Hot Folders
|   |-- Project 1
|   |-- Project 2
|   |__ ...
|-- 2. Cold folders
|   |-- Topic 1
|   |__ Topic 2
|__ 3. Archive

The first folder (Attachments) is for any media I'm using inside of notes. These could be images, audio notes, videos, or anything other than text.

The second folder (Hot folders) contains any projects I'm working on at the moment. These notes are so specific to a project that they don't serve any other purpose — think meeting notes or landing page copy. Your hot folders only contain notes you're actively working on.

The third folder (Cold folders) contains subfolders about subjects and things I'm not actively working on. These notes are "head pages" or pages where I consolidate other notes.

For example, let's say I have 35 notes about getting videos to rank higher on Youtube, I would create a subfolder called "Youtube SEO" and start bringing those notes together into an actual resource. This is good if you want to have an index of your notes and it can lead to some good insights.

The last folder folder(Archive) is for any projects that are completed. This is just so my hot folder map doesn't get clogged up with old projects

Those are the only 4 folders. All my other notes live in the root folder. It's a mess, but that's the point. Embrace the chaos.

Filling up your second brain with notes

Once you have the base structure in place, the important work starts — filling it up with notes.

The quality of your notes is going to determine the quality of your ideas. If you fill it up with garbage, you'll produce garbage. You want to pack your notes with as much value and insights as possible.

That said, don't be too restrictive. Otherwise, you'll end up with a beast of a note that holds everything.

The ideal note is short enough to read through quickly but holds enough value and provides enough context that it can spark an idea or move a project forward.

One of the dangers of note-taking — digital notes in particular — is the tendency to just copy-paste things into Obsidian and call it a day. This quickly leads to notes that a perfectly logical when you create them, but make zero sense when looking at them later on.

It's a bit like dreaming. When you're dreaming it's perfectly logical that to be medieval knight on a flying horse ordering a happy meal at the drive-in of a McDonalds on the moon, but once you wake up and think about the dream you can't help but wonder WTF you were thinking.

A good mindset to have is to act like you're writing an essay about the topic you're researching. This forces you to be critical about what you write down and it'll make it easier for you to spot holes in your arguments. Even if you're using it for yourself and don't plan on using it in a project, acting as if it's for a written essay helps improve the quality of your notes.

Linking notes together

You can fill up your entire second brain with notes and you'll get some benefit out of it. Its true power, though, is in linking your notes together.

When you build links to other notes, you're making them more discoverable, which in turn helps create serendipity. You might be looking at a note because you're writing an article, and stumble on a link to a note you made 2 months ago that helps you with a completely different project.

But linking to each note indiscriminately doesn't work well either. If everything is linked together, it's not valuable.

Put links in a context where they provide the most value. Links to book notes, for example, aren't useful when put all together. But if you're working on a project that requires a good system, a link to your book notes on systems thinking might be perfect.

When creating a new note, ask yourself a couple of questions:

  • What projects can I use this in?
  • How does this note relate to other notes?
  • In what context would I like to stumble upon this note?

Do this weekly and you'll be generating new ideas in no time.


With productivity systems, you run the risk of trying to find the perfect setup and end up getting nothing done. The same is true for building a second brain. You can easily spend weeks going from Obsidian to Roam to Notion and so on.

The key to this is to have a system that looks simple, useful, and intuitive to YOU. So don't be afraid to create something completely different.

The goal of all of this is to get better ideas and to be more productive, not to have the best system.