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8 Must-Know Hacks for Academic Note Taking in Obsidian

Recently, a colleague started note-taking with Obsidian. It was a revelation for me to see her struggle and face problems I never thought of before. In this post I want to give a few tips for beginners of note-taking and present some ideas that are not very obvious initially.

While note-taking seems obvious: “read and take notes”, organizing and finding your notes afterwards, is a big challenge because there are hundreds of ways you can do it and there is no per se better way to do it. Here are the main problems I see:

  1. How do I divide, organize, and structure the notes?
  2. Are there easy rules for a structure that I can do right away?
  3. What is the best software to use?
  4. How do I color-tag / highlight something (especially if you don’t know markdown)?
  5. What is a “pretty” format for my notes? Do I need it?
  6. What are plugins, and which ones of the 1000+ should I use?

If you have asked yourself any of these questions, read on! I will give tips on all of them and suggest a few useful tutorials for you to follow if you want to dig deeper!

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The first step is to be comfortable with taking notes. Only afterward does thinking of a larger structure and organization make sense. It brought me about three attempts of a few months each to nail down a system that works. But every system is personal, so my advice is to experiment at first and don’t burden yourself with too much high-level organization. Therefore, in this post we will focus on the basic elements of being comfortable with note-taking and Obsidian. My note-taking course (or free starter-sequence) have more information on how to structure your notes that you can check out after reading.

Let’s get started!

What is the best software for academic note-taking?

In my opinion, it is undisputed that Obsidian is the software of choice. It has all the ingredients an excellent note-taking app needs: Links, PDF embedding, a mature ecosystem of plugins for organization, integration with Zotero, and it stores files locally for speed and security. Plus, it’s free. It is by far not the only tool you can use. Logseq, Roam Research, Notion, Capacities, and Heptabase are alternatives, to name just a few.

Pros and cons of using Obsidian as an acaemic note-taking system.

All alternatives have pros and cons. For example, a similar workflow can be done using Notion and Notero, allowing much better integration with iPads. Another app I am keeping an eye on is Heptabase. It offers a more visual approach to information management. While Obsidian has a canvas feature, Heptabase uses nested whiteboards to structure information, plus its PDF integration is more advanced than Obsidian. Read all about the comparison of Heptabase vs. Obsidian in this article.

The most important thing to remember though is: “Good craftsmen never blame their tools“. Rather than thinking about the best tool, focus on mastering one of them.

Color-tag or highlight words in Obsidian

Something everyone is used to from a word processor like MS Word is that you can style every word in any color or font you want. Most modern note-taking tools are different for technical reasons. This results in much faster performance and higher cross-app compatibility. Most of them work in a format called markdown. This format interprets certain characters as formatting (see a full tutorial here). To add a highlight in markdown, you need to surround text in == like so:

Using the highlight feature in academic notes in Obsidian. Adds color highlights to text.

There is a plugin called “Highlightr” that you can use to add highlights in any color. But this comes at the cost of using HTML tags in your notes. When you edit the highlighted block, it will display a long string encoding the color.

Using Highlightr plugin to highlight words in different colors in Obsidian.

Use callouts to structure single notes

While markdown allows you to create headings, italics, and bold, it pretty much stops there. To add some more structure, you can use callouts. Callouts are boxes with different colors and titles. They can be collapsed to hide longer chunks of content. Here is a full reference on callouts. Don’t bother with the syntax; use the hotkey to add callouts. To set a hotkey, go to Settings → Hotkeys and set a hotkey for the “Insert callout” command.

Use callouts for structure in your notes.

Use properties to describe and summarize your notes

Despite being one of the most powerful features, beginning users don’t know properties because they are poorly reflected in Obsidian’s UI. If you imagine the file names of your notes in an Excel spreadsheet, it would be straightforward to categorize them by adding a column and calling it, for example, “category,” “date created,” or “importance,” right? This is precisely what properties are! They are pieces of (meta)information that you can add to your notes. Obsidian will not display them unless you are editing the note. Still, you can search for properties and, using the Dataview plugin, even automatically display a list of all notes having certain properties.

Properties make it simple to create very complex database structures in obsidian.

Which properties should you define, you might ask? This is a very personal choice for you. In the note-taking course for academics, we build a reference manager using Obsidian. For a reference manager, the notes are on academic papers, so we use properties you are familiar with from Zotero or Mendeley: Title, author, journal, and add some others like rating, summary, or when this paper was added.

To add a property, go to the top of your note and type in — (two minuses). Obsidian will convert this into an interface to add key-value pairs of properties. Here is how it looks to add an “aliases” property that stores synonyms for the title of your note:

Use the alias property to add synonyms to notes

Quite often, notes can have different titles. For example, biodiversity can be measured by counting the number of species or “Species Richness.” A more general synonym is “Alpha Diversity”. You might just write “SR” or “AD” when in a rush. Adding all these names as aliases to your note allows you to search for any synonyms and find the same note. Aliases are a property you can add to any note by typing in “–” at the top (see the video above).

Using aliases in Obsidian as synonyms to find notes easier.

By the way, this search dialogue in the image above is called “Quick Switcher.” Press CTRL/CMD + O to bring it up. Type in the name (or alias) of the note you are looking for to quickly open the note.

Stack tabs to get better overview

This feature is helpful once you are synthesizing information in your vault. To do this, you need to open many notes. Obsidian is technically a browser, so it displays open notes in tabs, and you can open multiple windows. Stacking tabs is a novel feature that allows you to scroll through your tabs rather than click on them. While it feels strange at first, it is beneficial. Here is how it looks:

Use folders and tags to categorize notes

I got asked this question often. I think using folders is more intuitive because this is how your filesystem works. But you quickly notice that some notes could live inside multiple folders. For example, if you make notes on paper, you can store them in a “paper” folder (by type), a “topic” folder (by content), or an “importance” folder (by relevance). This is where folders break down, and tags come in, as you can tag your notes by topic type or importance!

Tag sin Obsidian add additional structures to folders.

But too many tags increase the time it takes to tag a note and as you slack and forget your own system, duplicates or undertagged notes arise. This always ends in chaos, so you have to be careful with them too. My advice: “Use folders for broad unambiguous categories, otherwise use as few tags as possible”. A good balance means that your tags combine comparatively big groups of notes.

Too many versus too few tags in obsidian.

The general strategy for working with tags is simple: Designate a tag for a “project” you are working on and then use nested tags to identify different types of notes connected to a project. For example, a project can be #chapter1 (for Chapter 1 of your PhD). Nested tags would be #chapter1/meeting, #chapter1/reading, and #chapter1/question for separating notes on meetings, needed papers, or research questions relating to chapter 1. The benefit of nested tags have the benefit that you can find all notes (meeting, reading and question) by searching for the tag #chapter1 but also the specific notes. I go in-depth into how to structure your notes in the academic knowledge managements seminar and how to create automatic lists of notes with the Dataview plugin.

Use templates for your Obsidian notes

Templates in Obsidian are notes that live inside a particular folder. You can paste their content into any note using a drop-down menu and a hotkey. This makes your notes much more homogenous and forces you to add certain structural elements that you otherwise might be too lazy to add. A good example is a “Source note,” that is the note on a single paper:

Explanation on how to use templates for Obsidian.

I have made a tutorial on how to utilize templates on Twitter. It is really simple to set up Obsidian templates and there is an exhaustive repository of templates that can save you time or at least serve as an inspiration. My most used Obsidian note templates are:

  • Source notes (for notes on a paper)
  • Meetings notes (for notes during meetings with tasks)
  • Stub notes (adds Aliases to notes and a dummy tag reminding me that it needs tagging)
  • Project progress notes (whenever I complete a small part of my research and document it)

The Top 5 Obsidian plugins you will need

Obsidian has over 1500 community plugins, and it is absolutely overwhelming when you get started. But don’t be afraid; you don’t need plugins to gain a lot out of Obsidian. Use it without plugins first. When you feel comfortable you might notice that it would be nice to automate certain things or find a feature gap, whenever this happens you are very likely to find a plugin that solves this issue for you. Here are the top 5 Obsidian plugins and their use-cases:

  • Dataview: Allows to write queries that automatically displays notes and their properties as a list. This has countless use-cases. For example: A list of meeting notes belonging to a particular project, all papers on a specific topic or by a particular author and so on. Here is my 5 minute tutorial on using Dataview, the note-taking course has a chapter dedicated to Dataview and its use-cases.
  • Zotero Integration: If you want to import papers from Zotero this plugin is almost without alternatives. It imports your papers, annotations and meta-data into your Obsidian vault. Here is a tutorial on using Zotero Integration in Obsidian.
  • Kanban: This plugin allows you to organize your information in a drag and drop style board. A board consists of cads, which can be simple text snippets or notes. The cards live in columns representing a topic, importance or any other property. It can be used to organize project progress or sort papers. Here is a long tutorial with videos on managing your writing process with Kanban.
  • Calendar: This plugin displays specific notes (with a date in their title) inside a calendar. It is a helpful way to put meeting notes and ideas and document project progress. Here is how I use it to create weekly notes and plan out my week (also contains a tutorial on using the plugin).
  • Canvas: Canvas is a plugin that comes pre-installed with Obsidian. It allows you to lay out your notes graphically. If you need to synthesize information this is your go-to solution, here is a tutorial. Use it also for code documentation or to build arguments.

I also made a list of lesser known plugins that I find very useful and fun. Here is part 1 and part 2.


These tips are not an exhaustive tutorial for Obsidian, but learning should be fun. If you pick up one or two of these tips, it will make your note-taking much easier and more fun. On another occasion, you pick up something else in a YouTube video (there are a lot of great beginner videos for Obsidian out there). This way, over time, you master Obsidian. If instead you want everything at once in one extensive course, click on the image below:

Effortless Note Taking for Academics Banner

The tips presented in this article are:

  • Highlight words in your notes by surrounding them in == or use the Highlightr plugin to add any colors you want.
  • Callouts are an easy way to add stand-out boxes to your notes. Add a hotkey to add callouts in Obsidian. Callouts can be collapsed by default to tuck away unwanted text.
  • Use Obsidian’s “stack tabs” feature to scroll through dozens of tabs while synthesizing information.
  • Use properties to add summaries and metadata to your notes. Later, you can use the Dataview plugin to show lists of notes and their properties automatically.
  • Use the aliases property to give multiple synonymous names to your notes.
  • Use folders to group your notes into large groups and tags to fine-tune. Use as few tags as possible and prefer nested tags.
  • Set up a few templates to not waste time on repetitive formatting tasks and to ensure homogeneity across notes.
  • Don’t worry about plugins; start using them when you feel comfortable with Obsidian. My must-haves are Dataview, Calendar, Kanban, Canvas, and Zotero Integration.