In the series of articles about personal knowledge management, the previous was on the general motives and my recommendations when it comes to building a second brain. It was software-agnostic to focus on the core of what makes a good system. In this second article, I provide more specific recommendations on how to use Obsidian application. This is based on more than two years of experience, as of the time of writing, from using it for long-term memory management. I maintain a single database (called vault in Obsidian) containing more than 4,000 notes.

Because this would take so much time and make this article far too long, I am not going to teach you how to do things in practice. Instead, this article is here to help you discover the possibilities and limitations. If you are interested in practically getting started with Obsidian I recommend you to turn to the many specific tutorials which are available online.

For a fun introduction to Obsidian, have a look at this one minute cinematic trailer made by a user.

How I organize my Obsidian

I settled on Obsidian in January 2023, after two years of using TiddlyWiki as my first successful attempt in building a second brain. The reason was that Obsidian was similar but more powerful, especially for searching. It was easier to synchronize across several devices and the switch fairly easy. I did not like the markup syntax of TiddlyWiki notes, called WikiText, and preferred the more usual Markdown markup of Obsidian.

My previous experience revealed how things can get complicated when related notes are scattered across many places (databases). Therefore, I opted for a single vault system containing all the knowledge I want to keep over the long term. This greatly facilitates linking between my notes and searching for them. My notes are simple lightweight text files, so even though they are numerous, the Obsidian remains superfast. Moreover, it is sometimes difficult to draw clear boundaries between personal and professional life for me. Those are the reasons why I prefer working with a single vault system for now. Other users have different experiences (see discussion here).

The way I use Obsidian does not require many folders for structure. I think that having only an “inbox” and a “temp” are necessary, the rest can just lie in a third folder which could be called “content”. As of now, I still have several content folders, which is merely a legacy from my previous organization with TiddlyWiki which was based on several databases (i.e., TiddlyWiki databases are stored as separate portable HTML files). I have set Obsidian to automatically put new notes into the inbox folder, so I can focus on the note’s content itself and later think about the structure. My notes can be stored safely in any of those “content” folders because the relations to other notes actually define the structure.

Indeed, notes in Obsidian can be enriched with your own meta-data, supporting several different types (e.g., number, date, list of items). I have set mine to all have a “Related” property of type list which contains from zero to any number of links to other notes. Those links give context to the note. They somehow act like advanced tags because they are notes with their own content but which I can also use as entry-points thanks to the system of backlinks. This means that if note A’s “Related” property links to note B, then from note B I can see that note A refers to it. This replaces the folder concept and note B acts as one of the possible parents of note A. For this to work it is not even necessary to have the link to note B in a property of note A, in fact, it can be anywhere inside the note, it is just a way to make the relation visually clear for me.

For example, I could be looking for a quote from a book I once saved but cannot find via search. Therefore, I would turn to the book’s note and check the backlinks referring to it (provided that I mentioned the reference along with the quote). The backlink view also offers a way to have more context, not just the link to other files, so I can already look at the different content related to the reference. This way could spot the quote from the book note directly. See screen recording here.

Classic tags with the # sign are also supported. Similarly to note links creation, Obsidian provides suggestions while typing to make sure to avoid any typo. I use tags to mentions myself, putting warning to content when I do not trust it, giving action attributes to notes or content (e.g., #toReview, #toStructure, #needsReference, #toUnderstand, #toVerify). I am not a frequent user of tags because whenever it makes sense I tend to use notes instead of tags by using internal links.

Other Obsidian’s strengths

One of my favourite features in Obsidian is the ability to give aliases to a note’s title, meaning that a file can have as many names as you like. This is simple yet essential as previously described in the first article about second brain. Obsidian is one of the few applications out there today to offer such possibility, and I still wonder why this technically basic feature is not yet implemented in every software dealing with files. Now, I do not add an alias for all the possible names that a note could have (e.g., translations, synonyms). Often I start with the minimum set of that come out of my mind and which I would possibly use, in English and in French, then I would extend it with usage when I come across new names.

By default, Obsidian is free to use, it is shipped with most of the basic features and lets you install additional functions to complement them. There are currently two official plugins that are paid with a subscription-based model (Sync and Publish) but they also have free alternatives made by the community. In my opinion, paying for a plugin is more of a way to support Obsidian to run the company than the only way to unlock something. Obsidian advantageously grants academic, education and not for profit discounts so it is even quite cheap at the end of the day.

One of the key strength of Obsidian over other “modern” competitor software in knowledge management is its offline-first approach. I am not reliant on stable Internet connexion, which could be missing when travelling or having network issues, it is also much faster than having to exchange the notes over the Internet all the time.

Obsidian is extensively customizable. There are three different tiers to personalize according to at your taste, which come with gradual technical complexity:

• Tier 1: By default, it is possible to easily change some settings. This includes keyboard shortcuts, some elements in the interface and application behaviour. Obsidian also provides some core plugins offering additional functionalities, they can be enabled directly from the settings as well. This is the easiest way to adjust Obsidian to your needs, but it has a limited extent.
• Tier 2: On top of the official plugins, you can install third-party plugins and themes provided by Obsidian’s very active programming community. Those plugins bring plenty of options and really help to make your Obsidian work in the most ideal way for each of its users. At the time of writing, I have around 30 plugins activated and have tested probably close to a hundred since I started using it. The range of complexity varies greatly from one plugin to another. While some are more “install and forget” which directly apply changes, some come with additional adjustable settings, and others bring extensive customization options, still requiring you to implement them. Most of the plugins are free and open source.
• Tier 3: The possibility of developing your own plugin and to adjust the interface yourself via some code. This becomes interesting when you cannot find what you need from the many plugins available and provided that you are able to code. Obsidian is built on top of web programming languages. Therefore, plugins are written using JavaScript code, and you can adjust the style of the interface using some CSS code. Over time, I have added quite a few CSS snippets to customize Obsidian, either made myself or taken from others on the Obsidian’s forum.

Obsidian is cross-platform, at least considering the major operating systems (GNU/Linux distributions, macOS and Windows), while it is also available for both iOS and Android. The good news is that the mobile version is actually very similar to what you get with the desktop version, including support for plugins. This is a strong advantage for my use case, where I often use Obsidian on my mobile phone. Note that by default there is no syncing between devices, you either have to use a third-party cloud service to sync your notes or to pay for the official Obsidian Sync.

I am a keyboard person, satisfyingly various actions in Obsidian can be triggered with a hotkey, which are configurable. Even plugins bringing new functionalities generally offer shortcuts. It can be very efficient to use them for repetitive tasks like formatting. There is even a “vim” like key binding mode for the crazy folks out there!

As already mentioned, the notes are stored as Markdown files, which is a non-proprietary extremely interoperable file format and its markup syntax is supported by many applications. This means that moving out of Obsidian, if ever needed in the future, will be quite easy. Markdown is both machine and human-readable, meaning that if you open the raw file its content will be clear and editable, especially compared to other interoperable and open formats like HTML or OpenOffice documents. One can also insert HTML code for advanced formatting. Obsidian has support for LaTeX and ChemTex code for rendering maths and chemical equations. It also rocks code syntax highlighting for nice looking and easy to read snippets of code. Those are crucial for my use case at the cross-roads of science and programming.

On top of this, the file-based storage of Obsidian makes it possible to manipulate your notes from outside. For instance, I love to refactor my notes using a coding IDE like Visual Studio Code. The reason is that “search and replace” across the whole vault is not supported by Obsidian and I am very used to VS Code for programming. It allows performing advanced bulk edits based on regular expressions for complex patterns and transformation, while targeting only Markdown files in order not to break anything. Beware! Before doing this kind of wide edits, you should make sure to have a backup.

A great feature in Obsidian, is the possibility of inserting another note’s entire content or a fraction in other places dynamically, this is generally called transclusion. Using this you can virtually repeat some content in several notes while maintaining a single source of truth. If you edit the source, all embeds will reflect the change immediately (similar to Notion’s sync blocks or the <iframe> integrations on the web). See screen recording here.

Finally, similarly to programming IDEs, the layout customization capabilities are quite advanced. It is possible to open notes in tabs, split the window horizontally, vertically and both, you can also adjust the panes’ size. It is even possible to have multiple windows for a same vault, which is ideal when you have several screens. In addition, it is possible to activate a preview popup window showing the note content when you hover over an internal link. All of these make it possible to explore other notes, viewing them side-by-side, while maintaining the initial content visible to easily come back to it. This also works for exploring different portions of the same file. This is extremely useful for refactoring notes, for example when I want to see if there is any similar information elsewhere in my vault that needs to be grouped or linked. See screen recording here.

Cautions and limitations

Obsidian certainly comes with some limitations, which are often quite person dependent, but here is what you should be aware of:

• Despite its community oriented mindset, the Obsidian application itself is not an open-source software. The main issue is if the company behind Obsidian cease development without sharing the code, no one will be able to keep maintaining it. I hope that they will release the code in the future, following its major competitor, Logseq.
• All my notes lie locally on my devices as Markdown text files. This means that anyone curious and having access to my computer could read them in clear. Is that a big privacy issue? I do not share my devices except with the IT department of my institution when I get issues, and I lock my computer when I am away. I should enable storage encryption on my personal devices, so the files cannot be read without being logged in. Are the alternatives more secure? Not necessarily! Most of your apps (local or web based) do not require you to login all the time, so anyone using your device if not properly secured could access most of the information already, even though online exchanges would be encrypted. We do not even talk about how insecure are paper notes. Obsidian Sync uses encryption for transferring and storing the vault on their servers, the concern is about the note files that are stored on your device.
• You have to be aware that Obsidian is shipped with limited visual edition capabilities, you do not get a full-featured interface with a bunch of tool buttons. Instead, it tries to stick with what Markdown syntax has to offer, which is limited. However, you can install plugins if you like to have more visual editing palette with many buttons.
• Obsidian does not offer a real online service to access and edit your notes from a web browser. They have the official “Publish” plugin and also some free community alternatives to generate a website from a vault, but it is static. This could be a major limitation if you are often away from any of your personal devices having Obsidian set up. There is no portable version either, that would let you run the app from a USB stick for example. These limitations could cause some issues if you want to use it in an IT controlled environment where you cannot install and run unauthorized software at all. Personally, I am not really impacted by this and there have been attempts by the community to address those issues.
• Working with multiple vaults is possible, but having connections between them and searching across multiple vaults is not yet well-supported.
• In my opinion, and I have seen many similar comments, the big graph view offered by Obsidian is not that useful and feels more like a fancy gadget than a real breakthrough for knowledge management. While it is satisfying to look at my graph from time to time, I could hardly find any real use of this macroscopic scale overview. It can let you realize how much you are accumulating in your second brain, get to identify top linked notes, identify orphans or simply using it to showcase Obsidian to your friends and colleagues.
• The search function in Obsidian is strict about accentuated characters. As a French native, I use them quite a lot to name my notes, misspelled word would make the search not returning the right notes. This is also the case with words that are inflected depending on the sentence while still holding the close meaning (e.g., plurals, feminine forms). To cope with this I add alternative forms in note’s aliases and I try to use the plural form as much as possible as a naming convention. This is not so specific to Obsidian. The easy fix to solve this limitation is to install a plugin to replace the default Quick Switcher which can ignore diacritics, I use Another Quick Switcher.
• Obsidian does not maintain much metadata about files by default, in particular it does not keep track of created and last modified date internally. It rather relies on the underlying file system of the operating system, which can be subject to external changes, especially if you synchronize your notes on different devices. To cope with that, I use some plugins and template tricks to have the dates stabilized as two properties for my notes. They are useful for contextualization, but they can also be exploited in advanced search queries and for statistics. There is currently no automatic dating of the note’s content either. I often date content as part of the source anyway, except when it comes from published references where I use the publication date instead. Setting up Git versioning can also help to keep track of the changes quite precisely, with a granularity that depends on the backup frequency that you choose. I miss not having additional statistics like how many times each note is consulted to gain some insights of the most used notes and also the least for better prioritisation of my efforts.
• As a final warning, Obsidian has a rich ecosystem of feature to offer, both from its core functionality and community led additional features. Consequently, it makes the application both powerful but also potentially overwhelming regarding all the tools, techniques, tweaks to discover and test. It is easy to spend countless hours in customizing it. Avoid falling in the pitfall of overengineering, remain objective oriented, and it is OK to miss out many possibly cool features. This advice holds for many other productivity applications and methods available out there.

Despite those limitations, Obsidian remains the best fit for my needs and my experience showed that I can trust it on the long-run. I hope to stick with it for the longest time possible, so I can keep focusing on learning, remembering and producing interesting things rather than constantly spending time adjusting or switching applications and methods.

Notes on plugins

Before we move on to my plugin recommendations I want to give some warnings.

• It is of utmost importance to avoid creating strong dependence on community plugins. You should try to only use plugins for things that if it suddenly stops working (e.g., because of a bug or loss of compatibility), your system would not break. Community plugins are often maintained by a single person, who may stop at some point. If the plugin becomes no longer maintained, you may not have the time or technical knowledge to handle it on your own. Apart from that, having close to pure Markdown notes can also help if you have to switch away from Obsidian to another application in the future.
• Now, if you install a plugin, try to go for recognized plugins in priority. Avoid untrusted niches, especially those that you can only install from outside of Obsidian. On the contrary, community plugins which can be installed from the settings are verified by Obsidian, so you can expect them to be safer.
• Similarly, open-source plugins with large user bases are less prone to be abandoned. If development stops, other knowledgeable people can “fork” it and pursue development with an alternative version. This is possible both because there is a big community of software programmers using Obsidian.
• Limit the number of activated plugins, disable or uninstall others. Enabled plugins add up to the application loading time. They can also slow down the interface by running intensive tasks in the background.
• The idea is to avoid being a compulsive consumer of plugins, installing only the minimum required. You can delay the time when you want to install or implement a plugin, and wait until the need arises again several times, thus giving evidence that it is probably useful to find a solution through an additional plugin.
• How do I look and discover new plugins? There were plugins for almost any thing I needed, either offered as a core plugin or among the thousands of community plugins. Sometimes the plugin names are not obvious, so finding them from Obsidian by name can lead no relevant results. Using a search query on Google (or other search engines) which succinctly describes what I need have proved effective for me to discover plugins. You can also search directly on the forums (e.g., official forum, Reddit) and in the official help documentation. The trick is to use search keywords like site:obsidian.md or site:reddit.com. If this approach is not fruitful, you can post your request on the Obsidian forum, either in the help or in the feature request section, depending on the case. You can also ask your question to an AI, I found “Strange New Worlds” plugin in this way.

My plugins recommendations and use cases

All the plugins in this list may not be relevant to your needs, in such case avoid losing time in installing and testing all of them!

• Official “Core plugins”, maintained by Obsidian:
  • Sync (paid): This is a useful plugin that basically syncs my notes across my laptops (work and personal) and my phone. It only costs $28.80 USD per year with the 1 GB plan and the education -40% discount. This is also a way for me to support Obsidian development.
  • Outline: Shows the heading structure in the side pane. Allows to search for a specific heading. I have this opened almost all the time.
  • Search: Powerful full-text search across your vault’s notes. It has some advanced search options.
  • Note Composer: Utility to merge notes together and update links automatically.
  • Backlinks: Show the list of backlinks for the current note.
  • Command Palette: Opens a menu to search and run any command.
• Community plugins, maintained by external people (individuals or companies):
  • Git: I use this to do automatic versioning of my notes, I would rather not rely solely on Sync in case it fails. It is only set up on my work laptop, which is the device I use the most, and it pushes the changes in only one direction to avoid any merge conflicts. You should be careful not publicly putting unencrypted confidential data, my repository is hosted on GitHub and its visibility is private.
  • Templater: Helps to add automatic properties to newly created notes, including the creation date.
  • Settings search: This is a simple yet very useful plugin that simply adds a search box in Obsidian’s settings which allows you to search any settings with its name. It works for both core settings and plugin settings. It is a must-have if you often tweak your settings.
  • Another Quick Switcher: This is a replacement for the default Quick Switcher. It brings support for fuzzy search and can ignore accents and other characters variations.
  • Command Alias: As the name suggests, I use it to give short name aliases to commands comprising only a few characters.
  • Copy Block Link: Adds a right-click shortcut option and a command to quickly copy block or heading links, so you can paste it and embed them somewhere else in your vault.
  • Heading Shifter: Allows me to select some content in a note and make all headings inside the selection go one level higher or lower. It is very helpful when refactoring notes.
  • Hover Editor: This is a more advanced alternative to the default note previewer of Obsidian (core plugin) which opens a popup when you hover over a note link. You can change the popup size on the go, move and pin the preview window on screen to keep some context visible during some time without having to open the note in a side view or a new tab.
  • Image Captions: Allows to show the caption text of image links. I often put the image title and the source in the caption.
  • Imgur: When I paste an image, it offers me to simply upload it on my Imgur account and insert an embed in the note, thereby not consuming precious storage capacity for non-critical images.
  • Note dater: Add created and last modified date automatically.
  • Open Vault in VS Code: Adds a button and a command to open the note and the vault in Visual Studio Code, opening the possibility for bulk edits of notes that would otherwise be difficult to do directly from within Obsidian.
  • Recent Files: Adds a pane showing a list of recently opened files.
  • Text Format: Useful for cleaning copy-pasted text from the web and remove unwanted hyperlinks and formatting.
  • Strange New Worlds: My newest discovery, it shows a counter of referring notes to parts of the notes. I was looking for a way to know if a particular piece of content was referred in other notes before applying any changes to them that could have an impact (e.g., deleting, moving to another note).
  • Plugin Update Tracker: By default, Obsidian does not automatically update community plugins, nor does it notify you of their availability. This plugin notifies you based on specific minimum frequency. It also includes the possibility of delaying it to minimize the chances of installing a bugged update.