Note-taking: In search of the optimal system

For about 5 months I have been trying out different note-taking systems and applications, but only recently have I found the right workflow for me. I'm always updating it and experimenting, but it seems that I finally laid down the bases.

Let me quickly summarize what I learned during this journey so that you can learn from my experiences.

Choosing the tools

I started out using Notion, which has a great free plan and is growing rapidly.

All-in-one workspace,
Write, plan, collaborate, and get organized — all in one tool.


Although I really liked it (and am still using it to this day), it obviously had some flaws:

  • I spent more time customizing than taking notes
  • There is not yet (as of July 2020) an proper offline mode
  • I had limited control over my data
  • Does not have bi-directional linking (unless you do it in a clunky way) Bi-directional linking was recently implemented

I only understood why bi-directional linking is so important after I read the book How to Take Smart Notes (which I strongly recommend). It also encouraged me to take notes from books, articles and videos, since we in fact forget really rapidly about what we learned unless we practice regularly.

Side note: this is why spaced-repetition is so efficient when we want to memorize information.

Thanks to this book, I also discovered the Zettelkasten method, which requires a deep dive to fully understand it, but offers a novel way to approach note-taking I had not seen before.

I then managed to try quite a few apps, that I will list here:

Side note: a substantial list of note-taking apps can be found here.

What I ended up using is Obsidian.

A second brain, for you, forever.

Obsidian is a powerful knowledge base that works on top of a local folder of plain text Markdown files.


It works offline, lets you manage your data, has bi-directional linking, is free to use (see the details here), and allows me to focus more on content than organization.

Of course, it does not solve all my problems, that is why I am still using Notion (I will show you how shortly). I came to the conclusion that using a tool for something it has not been made for in the first place is often not worth the trouble.

For example, I have tried implementing a Zettelkasten-like method into Notion, which lead to my data being locked into a way too big database with un-exportable relational links between information.

I found that it is way better to use specialized tools for specific purposes than one tool which will supposedly solve all your problems. It allows you a lot more flexibility, as you can switch them easily. I believe there needs to be a compromise between decentralizing everything, which can lead to your data being too scattered around to make sense, and centralizing everything, which reduces flexibility and prevents you from finding a better way to do a specific action.

Now that I had found the right tools, I still had to choose a system to take notes.

Creating your system

When I started, I tried taking notes hierarchically with Notion. If you have read How to Take Smart Notes, you know it does not seem to be the right way to go, unless you want to build some sort of wiki. It is said to be better to start writing right away without worrying about the categories you want to put your note in. Then you add tags, links, … You can also read more thoroughly about it at

The core idea is to build your knowledge base from the bottom instead of from the top, that means the content you put in your knowledge base will naturally form clusters if the notes are well linked together.

So I started doing it the other way around: taking all my notes non-hierarchically with Obsidian. After a while, I noticed some sort of loose hierarchy is still useful when using Obsidian.

I think it's mainly due to the fact that Obsidian works on local folders. Sure, I could put all my notes and media files in a single folder called "Zettelkasten" or "Notes", and search from specific notes from there. But I find it more efficient to separate my notes, not with categories, but by type.

These are the top (and only) folders of my Obsidian notes:

  • Concepts: contains short notes which define a precise idea. They are strongly linked together and have multiple tags. An example of a concept note would be "Trust the process".
  • Essays: contains medium-sized notes of a personal reflection on a subject. They often refer to other type of notes. An example essay would be "Differentiate concepts and essays".
  • Files: contains all media files, like images or PDFs.
  • Inbox: contains recent notes which need to be sorted or worked on. An example inbox note would be a book I'm currently reading.
  • Daily notes: contains daily notes. I tend to write them elsewhere.
  • People: contains notes about people. It's here that I put the authors of the books I read, one note per person.
  • Resources: contains notes about resources I scrap on the web or elsewhere. This is mainly where my concept notes originate from. These notes could be about a book, a movie, a video, an article, a tool, … They are tagged accordingly.
  • Lists: contains notes listing information. These are often linked to the "resources" notes.

Because these folders describe broad types of notes, they almost never interfere (one note belonging to two folders), and therefore I don't have a hard time deciding where to put the note from the inbox.

Now I tried using only Obsidian for note-taking, but what really worked for me was using both Notion and Obsidian. I now use Notion for storage, clipping links and articles to a global database. This is also where I take notes from books, that I then "extract" to Obsidian as concepts. As I said earlier, I find it better to use specialized tools for specific purposes.

A comment of Dylan, on my Zettelkasten in Notion with Auto Footnote Backlinks video, sums it up very well:

Notion is great for general note-taking and logging data about your life / team. But Obsidian is better for Zettels. I'm thinking about using Notion to collect notes and Obsidian to process them into permanent notes.

Dylan Modell,


I hope you have got something valuable from this article. Tools may change, thus impacting our workflow, but the basic principles of linking notes and generally avoiding categories, once adopted, will steer us towards more thoughtful ways of organizing information, taking notes, and learning.

Please, if you enjoyed what you read, leave a comment below and share it with people that you know will enjoy it too.

Thank you for your time.

Updates from 2021: I found that outliners are what works best for learning. Logseq allows me to keep control over my notes while providing an outliner experience.