In today’s article I want to tell you about something that has significantly improved both my professional and personal life: organizing information in what is commonly known as a second brain.
Why organizing information matters
A few years ago, Alex, my ex colleague, gave me a book as a Christmas gift: Building a Second Brain by Tiago Forte (I’m not a sponsor of this book!). In it, the author describes a method he developed for organizing information in a digital space he calls the “second brain.”
Reading that book made me realize how scattered my information actually was: some notes on my phone, other stuff on Google Drive, bookmarks spread across different browsers, and so on.
Whenever I needed to find something — an article I had read, a reference I had saved — my first instinct was to try to remember the source, and then fall back on a Google search. An inefficient process that wasted time and rarely got me where I needed to go.
The PARA method
Before I walk you through my journey building a second brain, I want to spend a moment on the structure I chose.
There are countless ways to organize information, and many well-known frameworks to draw from ( PARA, “file over app”, Zettelkasten, GTD, etc..).
Picking one is a solid starting point.
What sets PARA apart from other methods is that it organizes information around the concept of actionability, divided into four folders (whose initials form the acronym):
- (P) Projects — everything with a defined deadline. I try to keep this folder to no more than five items.
- (A) Areas — ongoing activities and notes with no fixed deadline, things that are relevant to my life right now. This is where I capture ideas for new articles and write drafts.
- (R) Resources — long-term knowledge storage. I keep my current expertise, past experiences, and anything that might be useful later (home-related info, paint color codes, etc.).
- (A) Archive — anything that’s no longer active goes here: notes from job interviews, past projects, notes on obsolete technologies.
The book also covers the CODE method, a framework for distilling information down to its essence, capturing only what truly matters.
My first step in building a second brain was to set aside any temptation to tweak or customize the system, and instead follow it as strictly as possible. This let me validate a well-established method before introducing any friction of my own. Over the years I’ve made a few adjustments, but those came naturally through daily use.
My first second brain
I started with OneNote.
It was already part of my workflow (I used for a while as notebook at work) so there was no learning curve. It was free, and it worked across all platforms (Linux, Windows, Android, Mac), which was non-negotiable for me. I’ve never been tied to a single ecosystem, and my tools need to work wherever I am.
I ran my second brain on OneNote for over a year. There were quite a few limitations I tried to look past, keeping my focus on the methodology rather than the tool itself.
The limitations of OneNote
OneNote is a great note-taking app, but it falls short as a second brain. Here’s what I ran into:
Hierarchy
OneNote gives you exactly three levels of organization:
- Notebooks
- Sections (within a notebook)
- Pages (within a section — this is where you actually write)
This works fine for casual note-taking, but it’s a real constraint for a second brain. In principle, deeply nested hierarchies are something to avoid — but having too few levels was just as limiting. I personally never go beyond six levels, and I need that depth especially for my development and IT notes.
Linking between notes
Connecting notes to each other is central to any good second brain. My approach is to keep notes small and focused (one topic per note) and to turn any reference to something else into a direct link. This makes my notes dense with internal connections.
It also means I can abstract a note away from its original context and link to it from anywhere, regardless of where it lives in the hierarchy.
In OneNote, this was awkward and impractical. The tool is designed around notebooks and categories, not around free-form linking. My connections ended up being sparse and messy.
Vendor lock-in
This one is invisible while you’re using the tool, but hits hard the moment you want to leave.
Migrating out of OneNote is painful without dedicated migration tools. Notes are stored in an HTML/XML format that’s incompatible with Markdown. The more notes you accumulate, the harder it gets and you’ll likely have to manually revisit and clean up a significant portion of them.
When I eventually migrated to Obsidian (spoiler), I had to write a small cleanup script to fix formatting issues after importing my notes using Obsidian’s “Importer” plugin. (Thank you claude for your contribution at this step! 😁)
The upsides
To be fair, OneNote does have some genuine strengths, otherwise I would have dropped it immediately. 😁
Free with minimal restrictions
Simple, but meaningful: being free (aside from a few features locked behind an Office 365 plan) lets you learn and experiment with note organization methods without any subscription cost.
Spatial notes
A note in OneNote is essentially a blank canvas, a whiteboard where you can freely position content. Unlike a Markdown file, this gives you a lot of visual flexibility in how you arrange your thoughts.
⚠️ That said, this becomes a problem during migration: the spatial layout doesn’t translate to other tools, and the final order of content will need to be reviewed and fixed manually.
Automatic sync
Not something to overlook. I use my second brain across multiple devices (Android, Windows and Linux ) so having notes always up to date is critical. OneNote’s sync is genuinely fast and reliable.
The alternatives I evaluated
Before committing to Obsidian, I tested several tools, guided by these criteria:
- Preferably free
- If proprietary, data migration should be straightforward
- Flexible, free-form organization
- Available on all my platforms (Android, Linux, Windows, iOS)
- Easy to access both at home and at the office
Here’s what I looked at:
Notion
- ❌ Preferably free
- ❌ Easy migration out
- ✅ Free-form organization
- ✅ Cross-platform
- ✅ Easy access from anywhere
Notion is an impressive platform, but I ruled it out for two reasons: migrating away from it is non-trivial, and the free tier capped file uploads at 5MB — which was a dealbreaker for me.
Affine (self-hosted)
- ✅ Preferably free
- ❌ Easy migration out
- ✅ Free-form organization
- ✅ Cross-platform
Since I run a homelab, I tested Affine PRO self-hosted and was genuinely impressed. I liked the idea of keeping full control over my data. The sticking points were practical: accessing it from my work PC would have required a VPN, and same when I was out and about. On top of that, migration out looked like it would be just as painful as with other proprietary formats.
SiYuan
- ✅ Preferably free
- ✅ Easy migration out
- ✅ Free-form organization
- ✅ Cross-platform
I really liked the philosophy behind SiYuan — it was the closest competitor to Obsidian right up until the end. Why did Obsidian win? Keep reading. 😁
Obsidian — my (new) second brain
- ✅ Preferably free
- ✅ Easy migration out
- ✅ Free-form organization
- ✅ Cross-platform
A few things pushed me toward Obsidian:
- Notes are stored as plain Markdown files. If I ever want to switch tools down the road, the path out is clear and painless. No vendor lock-in
- I’m a developer — I can write custom plugins if I ever need functionality that doesn’t exist yet.
- I can manage my own backups, or rely on Obsidian Sync if I prefer to keep things simple.
Migration time
The full migration took me almost two weeks, from moving all my notes over and reorganizing them. I also wrote a small tool with Claude Code to fix some formatting inconsistencies and title casing issues.
Conclusions
This article has been a summary of my journey building a second brain: from scattered notes everywhere to a system I actually trust and use every day.
Would I give it up? Absolutely not.
Having a second brain remains, for me, essential, even in a world dominated by AI, where you can get a (fairly) reliable answer to almost any question in seconds. My second brain is where I keep things I’ve personally tested, experienced, and learned. It’s a trusted space I can turn to without any doubt about the accuracy of what’s there.
If I could go back to my school years, one of the best pieces of advice I’d give my younger self would be: start building a second brain as early as possible.
