How to organize notes in Obsidian knowledge base - best ways to organizing your effective system

How to organize notes in Obsidian knowledge base - best ways to organizing your effective system

I have been using Obsidian for a long time to create a Second Brain system. An important task I had to solve was to properly organize the storage of notes in the repository. In this article I want to collect popular concepts of organizing notes, tips, review of Obsidian features and share my observations.

Ways of organizing

Let's imagine that we have a repository with a large number of text notes and subfiles. All of them are in one folder, unconnected and unstructured.

If there are 5-10 such notes, it is still possible to navigate. 50-100 — it is more difficult to work efficiently, but it is also possible. But if there are 500-1000 notes, you will not be able to work productively.

Let's look at the basic ways you can organize these notes to make it easier to add new ones, edit, search and view the information you need. For this example, I'll create a new repository with generated notes.

picture — obsidian repository with lots of unstructured notes


I think folders are the core of any digital organization. You can think of folders as drawers for storing things. You would probably put socks in one drawer, tools in another, and food in a third. I hope the analogy is clear — folders can be used to group notes or files that are similar in type.

But folders have a big disadvantage — no flexible structure. For example, if a note refers to several topics at the same time, you will have to limit yourself and choose only one. In addition, it is difficult to navigate through them, especially at a high level of nesting.

Therefore, folders should not be used for detailed structure. For this purpose, tags, which I will describe further. Just fix in your head that folders are not a flexible structure that we use only at the basic level of distribution.

And just at the basic level, this disadvantage can be used as an advantage — notes from different areas of your life are clearly separated from each other, making them easier to see. For example, it's inconvenient to keep work files and home shopping lists in the same folder.

Next I will describe one of the concepts, PARA — folder allocation to projects, areas, resources and archives. You can take it as a basis and refine it to suit your preferences.

Remember our test repository with notes in one folder? Now I can create 4 folders and distribute notes in them — work notes to projects, attachments to resources and so on. The repository will become much cleaner and tidier. But at the same time I remember not to create too many folders, so as not to lose flexibility.

picture example of creating folders using the PARA method


As I wrote above, for detailed categorization of notes it is more convenient to use tags — special labels, like colored paper labels that you can stick in your notebook.

Tags are more convenient than folders, because you can attach an unlimited number of tags to one note.

You can also search tags, create nested tags, and quickly rename them — I wrote more about all the features in the article about using tags in Obsidian.

Let's tag the notes in our test knowledge base — a handy structure will appear in the tag tree panel.

example of tagging notes in obsidian knowledge base

If you click on a tag, you will see all notes with that tag in the search panel:

картинка пример поиска по тегам в obsidian

You can also enter multiple tags to see notes where those tags overlap.

картинка пример поиска по нескольким тегам в obsidian


An important feature of Obsidian, like any knowledge base, is the ability to create links between notes. If another note describes in detail a topic covered in the current note, don't forget to link to it. 

By creating such links, you create a network of interconnected information, which helps you understand and recall context and find new ideas. This is one of the basic principles of the Zettelkasten method, which we will also consider next.

Obsidian has a convenient tool for viewing links between notes — a visual graph.

visual graph in obsidian

By the way, you can enable it to display tags as individual points.

displaying tags in visual graph in obsidian

In the sidebar panel, you can see incoming and outgoing links for the current note — sometimes this is useful.

incoming and outgoing links for the current note in Obsidian app

My combination

Each of these methods has advantages and disadvantages:

  • Folders can separate notes and files from different areas of knowledge, but break the flexibility of categorization
  • Tags give you the flexibility to categorize and search for notes, allowing you to create clearer links
  • Links connect notes right in the content, give you deeper context and useful information, but they can't structure information on their own.

The conclusion I've come to is that you should use all three methods, but for different purposes.

I use folders to categorize different types of files, projects or areas of knowledge. If everything is in a single folder, you can't work effectively with a file tree.

I used the PARA method as a basis for the folder structure, but in Obsidian you may also want to use the «Templates» folder to save frequently used blocks in the Templates plugin. This is one of the must-have plugins for Obsidian. Although it can be placed in «Resources».

You can create a separate «FILES» folder for attachments, or use the «Resources» folder from PARA. If you want to keep daily notes, use the «DAILY» folder. If you like Zettelkasten method, you can create a folder «CARDS», which can replace the «Areas» folder from PARA.

My working organization structure looks like this:

    Project 1
        Project files
    Project 2
    Note 1
    Note 2
    Note 3
    Note 4
    Useful files
    Attachments for notes
    Old projects
    Old files

As you can see, instead of the Areas folder from PARA, I use a card file folder with a flat structure from ZettelKasten. All notes are in one folder and do not use subfolders.

I did it like that, because I get a lot of notes and folders, and it was very inconvenient for me to search through the file tree. At one point I was simply afraid to log into Obsidian to avoid the stress of this structure.

It's better to write a note intelligently (in particular, write keywords well and a lot) and use Obsidian search — it works pretty well. I'll describe this in more detail later in the section on note layout.

I use tags and links wherever possible — try to tag the post and put links right away so you don't forget later.


There are also frameworks and useful tips for organizing a knowledge base that can improve the process of managing and using it.

Flat structure

Flat structure is the storage of all notes at one level, without nested folders. This can be effective when combined with a tagging system. This method provides flexibility and eliminates the need to navigate through folders.

But it is not useful for a large knowledge base with different directions — I wrote about this above in the section about folders. Then you can create a flat structure in one of your base folders. In my example, this is the «CARDS» folder with notes using the Zettelkasten method.


It is a German term meaning «slip box». The methodology was developed by the German scientist Niklas Luhmann. He kept a large card file of his ideas and knowledge. Each card contained one idea and had a unique number. The cards were linked to each other by this unique number and did not have a folder structure.

Thanks to this method, Niklas wrote 158 books and several hundred research articles during his lifetime. I think it certainly deserves respect.

In the future I plan to write a detailed review of this methodology, but now let's look at its basic principles:

  • Atomicity and autonomy — each post should present only one complete idea and fully disclose it. This allows you to avoid duplicating ideas and quickly absorb information.
  • Linking - all notes should be linked to each other. This allows you to build new links in your head, to dive into the information context faster. Notes without links are easy to lose forever. When creating a link, you need to explain why it is placed here. 
  • Flat structure - all notes are stacked in one folder. Navigation is realized by unique identifiers and links.

More can be emphasized as optional points:

  • Write in your own words to understand the topic better and get into it faster after a while
  • Do not delete old notes and do not be afraid to add new ones.
  • Writing is easy when the idea is ready, don't overcomplicate it

Through this method, you help develop your second brain and the interconnectedness of ideas, which makes it easier to identify patterns and generate conclusions.

In modern realities, when we maintain our knowledge base in an app, you can transform this method to suit yourself — use tags, for example.


As I wrote above, this method involves structuring the files in the database into projects, knowledge areas, resources, and an archive.


Creating content maps — notes that provide a list of links to other notes. This technique was also used in Zettelkasten.

Personally, it didn't work for me, because it's faster to search for notes using search, and content maps need to be updated and searched too.

But MOCs can serve as a good starting point if you want to detail an area of knowledge — make a list of topics and content in the map and refer to them as you write.


Create a basic «entry point» to your knowledge base — a page with links to all the most useful pages. This is a global content map like the homepage of a website.


For storing ideas that are not fully formed, which you can come back to later and fully transfer to filing cabinets or projects.  Useful method, sometimes you need to save some text, a checklist, a link to a website or an image. 

But I decided that it's not always convenient to do it in Obsidian, so I use Google Keep and then transfer the information to Obsidian as needed.

Note structure

Note layout and content can also improve the process of organizing your knowledge base. Here are some tips:

Use headings

In addition to a first-level header, you can break the note into multiple sections and subsections — just as this article is broken down, for example. This makes the content easier to navigate and digest.

Outline panel

If you follow the last tip about headings, Obsidian has a document headings navigation panel — use it.

note content panel in Obsidian


For me this is a very important point, because I lost a lot of time not using it, and greatly simplified my life when I realized how I should use it. If you write the keywords of a note when you create it — it will be very easy to find it later through search. Much easier than digging through tags or the file tree.

You create your own search engine, like Google, which does not search the entire Internet, but only your knowledge base.

The downside of this search engine, unlike Google, is that it doesn't understand synonyms and variant spellings, so we have to take care of that up front.

Make a list of words by which this note can be found in the future. Don't rely on a headline — in a few months it will completely fall out of your head, and the search query will most likely be formulated differently.

You can specify keywords after the main content as text or in a special YAML markup block at the beginning of the note. I use the first option more often so that when I reading the note, I can check if the keywords are correct.

Identifier and date stamp

One of the disadvantages of Obsidian for me is that, while it is convenient to link notes within the program, you can't link to a specific note from the Internet, as in Notion, for example.

You can partially get around this limitation in a clever way — add a unique identifier to the note header, and link not to the note, but to the search by this identifier.


I use a timestamp of format { year month day hour hour minutes seconds } as the identifier — for example, { 2023081413135723 }.

So the identifier is very likely to be unique, because you are unlikely to create more than one note per second. And it contains useful information about the time the note was created. Then the search link will look like this:


You can use it anywhere, including in your browser and other note programs — just click on the link and the Obsidian app will open up with a search for that ID, with the note we want at the top:

timestamp search example

This was an important discovery for me because most of my work happens in a browser, and I'd like to be able to use external links to my Obsidian base.

Obsidian tools

Obsidian provides several tools for easy note management. Let's review them.

Visual graph

Already described it above. It is a graphical representation of links between notes and tags in the form of a scheme. From practical usage — it is convenient to find «lost» notes without links. And to get aesthetic pleasure from viewing your graph.

Tags tree

Allows you to quickly navigate through tags. With TagWrangler plugin installed, you can manage and rename tags very conveniently.


Search is a very powerful tool if you prepare your notes for it. Take care of it and do it right away when you create a note (I mean keywords) — gradually search will become your best friend.


I tried to collect all the useful information in this article and give examples of how I personally use these methods. Obsidian is very flexible and allows you to customize the process of knowledge base maintenance as it is comfortable for you, so you can try all methods and make a combination for your needs. Good luck with your knowledge base maintenance, and thank you for reading this article! 

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