Good research relies on good notes, so it’s imperative to choose a note-taking app that suits your research needs. Here, we compare Notion vs Obsidian, two of the most popular note-taking applications available, and see how they stack up when it comes to doing productive academic research. If you’ve never used either yet, don’t worry. We walk through each tool’s key features, and how they compare for common research tasks. Let’s dive in!
Learn the foundational systems researchers are rarely taught: from powerful note-taking and knowledge management methods to modern lit review tools, ethical AI and productive research workflows.
Why Choosing the Right Note-Taking App Matters
Practically all students, academics, and researchers have a note-taking system. Whether it’s pen-and-paper, jotting down ideas in Apple Notes or MS Word, or using a robust, inter-connected system of linked knowledge (i.e. the EA note taking system), we each have our own unique system. The type of system we use can greatly impact the quality, productivity and even the success of our research.
For example, here’s what an EA Member recently shared based on their experience with a note-taking class, “I really feel like I have a system that I can use to finally start organizing my information and maybe I’ll even be able to get more efficient at turning that info into new presentations, writing, and scholarship.” This hits the nail on the head when it comes to note-taking systems: being able to efficiently transform your knowledge efficiently into scholarship, presentations and real-world impact.
Which note-taking app we use plays a key role in how we can organise our research, build understanding, generate ideas and eventually write finished assignments or papers. App that lack features will slow us down, require extra hours of tedious work, and perhaps reduce the quality of our work if we can’t find the right references or get an accurate view of our research. Using an unsuitable tool risks losing good ideas and potential opportunities. In the long-run, this may start to slow down our career and inhibit our growth. That’s why it’s worth spending a bit of time up front to choosing the right note-taking tool, and hopefully this Notion vs Obsidian comparison can help!
What Academics Need From a Note-Taking System
For anyone doing research, we have distinct note-taking needs. This is true whether you’re writing your first literature review as an undergraduate or managing international research collaborations as a senior academic. For anyone doing research, here are some of the key ways our note-taking system should support our thinking:
- Build understanding of topics and sub-topics
- Remember what we’ve read, watched or learned
- Quickly find our previous notes on topics and ideas (even if we wrote it down months ago)
- Quickly find any academic paper we’ve read, whether it was last week or last year
- Write manuscripts based on our notes, without messy back-and-forth
- Cite relevant papers in our manuscripts, based on our notes and saved papers
- Integrates into our bigger research workflow, without us jumping between apps and systems repeatedly
- Manage different projects, papers, and collaborations
- Manage large, complex and long-term projects that may last years (PhDs – we’re looking at you!)
Does your current way of taking notes do all the above?
If you answer “no”, then you may have a lot to gain from switching the note-taking app you’re using to one that does support all of these. We’ll be sure to examine all these requirements below as we compare Notion vs Obsidian for academic note-taking.
Obsidian vs Notion: Key Feature Comparison
Notion has over 100 million users and is popular among students, academics and researchers. Although Obsidian is also a popular note-taking tool, it’s certainly less well-known than Notion and has anywhere from 1-10 million users. Both are robust note-taking applications, and have a much wider range of features than lightweight tools like EverNote, Google Keep, or Apple Notes.
Overall, the key differences between Obsidian and Notion are in how customisable and expensive each one is. If you identify as a self-starter, keen to build things yourself, have control of your data and like free tools that don’t lock you into any particular structure, you’re likely to opt for Obsidian. On the other hand, if you like polished software that’s ready to go out-of-the-box, appreciate built-in features, and don’t mind less customisation and some potential cost, you may prefer Notion. What best summarises this is the number of plugins each app has: Obsidian has 2,700+ Plugins in Obsidian, whereas Notion has just over 200 integrations.
We compare both tools over a range of key categories and review the key differences below.
Note Files: Obsidian Notes vs Notion Pages
The core file structure of a note-taking app is important to consider. This determines how easy it is to access notes, how well it scales with 1,000s of notes, and how much control you have over privacy or security. Notion and Obsidian differ fundamentally in how data is stored and accessed.
Obsidian
Obsidian functions only as a desktop application. Each note in Obsidian is a file stored locally on your hard drive. It never leaves your computer if you don’t want it to, giving you maximum control of your notes’ privacy.
Notion
Notion stores your notes in the Cloud (using AWS), and this is true whether you use the online version of Notion or the desktop version. The notes themselves are actually stored as blocks in databases (we’ll look more at what these “blocks” are below). You can edit notes offline, and re-sync them once back online. Some may find it convenient to access all their notes in the browser. If you’re working on classified research or need to follow certain rules regarding security, you may need to evaluate if a cloud-based tool like Notion meets your requirements.
Tables: Obsidian Bases vs Notion Tables
Creating tables in your notes is a key functionality that comes in handy for many different purposes throughout a research project. You may make tables to keep track of papers, distinguish studies, reviews results, or organise knowledge for some other reason. Both Notion and Obsidian offer a strong solution for tables, and offer similar functionality.
The main difference between Obsidian Bases and Notion Databases is what data they’re built on. In Obsidian, Bases consist of notes, and no column or value can be edited without also changing the original source note. Notion Databases, on the other hand, are more like tables, which you can build from scratch with the option to link notes within columns.
Obsidian
Tables in Obsidian are called “Bases”. This is a relatively new feature (as of 2025). Obsidian Bases let you view notes in a table-format, based on filters. The filters can be done using Tags, Folders or other attributes of the notes. You get the ability to customise how the notes are displayed and which columns these tables have. Entries are directly editable, meaning that when you edit a row of the table, you’re editing that “source note” too. Additionally, you can set up context-dependent bases which function like templates for bases, and have no equivalence in Notion.
Notion
Tables of notes in Notion are called “Databases”. Just like the Bases in Obsidian, these let you link other pages in the results. Databases in Notion are extremely powerful and flexible, offering a range of filters, grouping, etc. as well as setting data types. The rows in Notion databases are more like rows of a table, and you can link notes in particular columns. This is slightly different from Obsidian bases, where the rows themselves are the notes themselves.
👉 Learn more about using Obsidian Bases for academic note-taking here.
Formatting: Obsidian Markdown vs Notion Blocks
How you format your notes is largely a matter of personal preference, technical proficiency and how you plan to use your notes later. For example, if you plan to copy-and-paste text from notes into manuscript drafts in other software, you may want the formatting to remain consistent. Otherwise, you’ll need to redo each italic, bold, header, etc. that you created in your notes.
The good news is that both Notion and Obsidian let you export your notes as Markdown. The benefit of Markdown is that files are stored as plain-text and can be easily read by many different apps. This makes it easy to import/export or copy-and-paste, while retaining formatting.
The main formatting difference between Notion and Obsidian is that the entire Obsidian experience is in Markdown, whereas in Notion you have a block-based editor.
Obsidian
Obsidian notes are formatted using Markdown. Markdown is a way to program text to appear different ways. If you’re unfamiliar with Markdown, there may be an initial learning curve. For example, to make a heading you type in a #, to make something bold you surround the text in asterisks: **bold**. You can download certain plugins and create custom rules in Obsidian to make it easier to use, and to “bring back” some of those familiar editing tools. For example, the cMenu plugin.
Notion
Notion has a standard visual editor, and the experience is like an easy-to-use writing software. It will feel a lot like MS Word, Google Docs, EverNote, etc. That means you can highlight text and choose how it appears using buttons (highlighting, colours, bold, and so on). Notion also understands Markdown and can export files in a range of formats including Markdown.
Calendar: Obsidian Calendar vs Notion Calendar
There are many ways researchers may incorporate time and dates into notes. Whether it’s to keep track of daily progress in a research journal, to record when sources were pulled, or to set project timelines and to-dos, having some calendar functionality is essential.
Both Obsidian and Notion offer calendar functionalities and record-keeping.
Obsidian
Obsidian, by default, doesn’t have any built-in calendar system (other than an option to create a “daily note”). However, it has a range of plugins that provide different calendar and date functions. There are various Calendar plugins to explore, such as the Calendar Plugin which allows you to display Daily Notes in a calendar or the Full Calendar Plugin which helps you manage events and notes in your vault. You can also add date attributes to Notes, and filter for these in the Bases to create custom views based on dates.
Notion
Notion has a few different calendar options. The “Notion Calendar” can link to your personal calendar (i.e. Google) as well as to tasks and notes you have in Notion. You can also create Databases with a Calendar View. This is particularly handy to keep track of deadlines, progress, and a range of time-dependent research tasks.
Of course, calendars are just one way to keep track of time and deadlines. Another important aspect of both Notion and Obsidian is that notes have time-stamps and date attributes, allowing you to sort and access notes by date.
Search: Finding Notes in Obsidian vs Notion
Notes are only useful if you can find them later. Searching and accessing notes may seem like a simple task, but it can quickly get complex depending on what you’re looking up. For example, you may remember reading a paper on topic X, but struggle to find it if you forgot the author name and title. Even if you found the note you took on the same topic, you may not find the original paper if you forgot to reference it in that note.
Searching through notes depends both on the software you use and how you take notes. The Effortless note-taking system is built on certain connections between topic and source notes, to ensure you can always find the source your notes are based on.
Both Obsidian and Notion offer similar global search look-up, as well as linking, so you jump between notes and find sources quickly (assuming you set it up that way).
Obsidian
Obsidian uses a global search feature for all notes, in the left side-bar. You can customise your search, run advanced queries and embed search queries into notes. Aliases are an Obsidian-unique feature, allowing you to search for notes based on custom nomenclature. You can filter searches to a specific folder, tag, or property. For example, you may want to see all the papers you’ve collected that were published in a certain journal. You can use the Floating Search Plugin to navigate your vault more easily. You can also use the Smart Connections Plugin to search on notes using AI.
Notion
Notion has a global search feature across notes with several filters (title, created by, folder/file, and date). It’s accessible in the left side-bar, just like in Obsidian. You can also search your notes using the built-in Notion AI. For example, you may ask for all your notes on a particular topic or all the source notes you have for papers addressing a particular research question.
Organising: Linking Notes in Obsidian vs Notion
Linking notes together is the difference between taking notes versus building a knowledge network that helps you learn. You may be reading about Topic A, which connects to Papers A, B and C, as well topic B and sub-topic S. In the ideal world, each of those components has its own note, and they are all inter-connected so you can jump between them as you review your notes. This keeps your understanding organised and clear, instead of dumping all your knowledge into one long document. It’s arguably the most important component of any note-taking system.
Both Obsidian and Notion offer strong linking abilities, allowing you to connect notes, ideas and sources easily.
Obsidian
To link to a note in Obsidian, you use the [[ NOTE_NAME ]] format. After typing the initial brackets, “[[“, Obsidian will automatically provide a list of notes that you can search on and add. Obsidian has the added benefit of allowing deep-links to PDFs with the PDF++ Plugin. This lets you hover over links and see your annotated PDF immediately.
Notion
To link a note in Notion, you type “/link” and select “Link to Page” from the set of drop-down options. Then, type in the note name, or search for it in the next drop-down. Although Notion allows you to embed PDFs, they are treated more like an independent data object. If you wanted to annotate the PDF, you’d need to re-upload it for those changes to “stick”.
TeX & Math Equations: Obsidian vs Notion
For some domains, keeping track of equations in notes is non-negotiable. Thankfully, both Notion and Obsidian make it easy to insert equations into notes.
Obsidian
To create an equation in Obsidian, use the $$ EQUATION $$ format, where the equation is written in TeX style.
Notion
To create an equation in Notion, type “/equation” and select either “Block Equation” or “Inline Equation” from the options. Enter your equation directly in the prompt in TeX style.
💡Tip: If you find yourself spending too much time transcribing equations into TeX, it’s worth knowing about Mathpix. This desktop tool lets you screenshot equations and immediately get the corresponding TeX.
Plugins & Integrations: Obsidian vs Notion
A note-taking application is one of many tools you use to support your research. If your notes aren’t well-integrated into the rest of your workflow you can end up wasting hours just moving data between apps. Many researchers need to use notes alongside a reference manager (Zotero, Mendeley, EndNote, etc.), writing software (MS Word, Google Docs, LaTeX), AI (ChatGPT, Consensus, SciSpace, etc.), and a host of other tools.
Overall, Obsidian offers significantly more Plugins than Notion. You can access 2,700+ Plugins in Obsidian, whereas Notion has just over 200 integrations. This is because Obsidian is designed to be customised and tailored to each user’s preferences using plugins. On the other hand, Notion users tend to just use Notion out-of-the-box, and rely much less on customising via plugins.
Obsidian
Obsidian is highly customisable and has a library of 2,700+ Plugins. These include integrations to other software tools, as well adapting the interface and tools within Obsidian. See some of the best Obsidian plugins for academics here.
Notion
Notion is quite robust out-of-the-box, but has also a small library of around 200 integrations. These help you connect Notion to other software tools like Outlook, Google Calendar, Gmail, Slack, etc. There are also some independent plugins for Notion, but no centralised “plugin store”.
Zotero Connection: Obsidian vs Notion
Both Notion and Obsidian have plugins to integrate directly with Zotero, a popular reference manager. This makes it easy to keep track of references in your notes and connect ideas directly to the original source. Quickly accessing source PDFs is essential when it comes to writing up a paper, and needing to see the sources your notes are based on.
Obsidian
To sync Obsidian with Zotero, use the ZotLit Plugin. You can automatically creates notes for each paper in Zotero. Check out our guide here for how to get set-up with ZotLit.
Notion
To sync Notion with Zotero, use the Notero Plugin. You can automatically creates notes for each paper in Zotero.
Want to set up Obsidian with Zotero? Check out our in-depth guide on using ZotLit here:
👉 Connecting Zotero and Obsidian with the ZotLit Plugin + Templates
Performance: Obsidian vs Notion
Depending on your project, you may end up with 100 or 1,000s of notes. It’s key to consider which system can truly scale with your knowledge for years to come.
Both Obsidian and Notion can scale to managing 1,000s of notes, but you’ll notice different performance drawbacks. Obsidian tends to load slowly for big vaults and it can take a long time to synchronise shared spaces. But, once up and running, Obsidian tends to work relatively reliably and quickly, no matter the vault size. Notion, on the other hand, loads fast no matter how large the project is. But, the browser version may fail or crash unexpectedly, requiring you to experiment with different browsers or trouble-shoot using the online community or Reddit. Large and collaborative spaces are more likely to cause these issues than lightweight, personal collections.
In theory, Obsidian ought to work faster than Notion because the files are stored in Markdown locally, making them faster to access than Notion’s cloud-based files. However, your personal experience and experimentation is going to be the best judge of which one works faster in your case.
Price: Obsidian vs Notion
Although at the bottom of the list here, price can be one of the most important criteria for academics when it comes to selecting a reliable tool. You may be have a certain budget allotted for tools, or you may be steadfast in not wanting to pay. Cost is one of the biggest difference between Obsidian and Notion.
Obsidian is always free, whereas Notion is free up to certain limits. You’ll want to consider the scope of your research project to see if you’ll end up hitting these limits. Once you’ve hit a limit, you’ll need to pay for a monthly subscription.
Obsidian
Obsidian is free, always.
There are no hidden costs or blocks on the free version. You can collaborate for free as well by sharing vaults on the cloud (for example, Google Drive). The only paid feature is Obsidian Sync which syncs vaults across devices (i.e. desktop and mobile). However, you can “hack” around this using Google Drive.
Notion
Notion is free, up to certain limits. Advanced features like unlimited AI use, collaboration, or uploading files over 5MB all require being on a paid subscription. See the pricing page for details.
Visual Notes: Obsidian Canvas vs Notion
Notes don’t have to just be text. Mind maps (or sometimes called whiteboards) are a powerful, visual way to interact with your knowledge at scale. In Obsidian, this is a built-in feature called Canvas, which lets you manage projects or build Mind Maps using your notes. It’s relatively unique to Obsidian. For most other note-taking software, you can instead build these maps using other visualisation tools (like Draw.io), and then embed them as images in your notes.
Obsidian
Obsidian has built-in visualisation capability to create Mind Maps called Canvas. You can use these to keep track of research projects or to store insights and build arguments for your research. Your notes are like elements on the canvas which you can connect, annotate and build off of.
Notion
Notion doesn’t have a built-in feature like the Obsidian Canvas, but you can use Mindmap.so Plugin. With Mindmap.so, you can create whiteboards of Notion pages and databases, like the Obsidian Canvas. You can also build visualisations in other tools (like Draw.io) and import them into Notion as images.
👉 Learn how to structure research arguments using Obsidian Canvas
Notion vs Obsidian for PhD Students
When it comes to thesis writing, both Obsidian and Notion can support big collections of notes, sources and linked knowledge. Which one is better depends largely on your personal preferences, budget, and how much customisation or flexibility you expect. Many PhD students on a budget tend to go for the “free” option, and try to avoid any software that may lock them into a monthly subscription. If you think your project needs will exceed the free Notion plan, then it may be worth using Obsidian instead, which remains free forever.
What sets a PhD apart from other research is that is often the first long-term research project you’ve worked on. This means that you’re not only learning about your subject domain, but also how to organise your knowledge efficiently. Check out our free note taking course to see exactly how to build out a scalable knowledge system in Obsidian.
Is Obsidian Too Complicated for Academics?
One of the biggest challenges researchers have when using any tool is the complexity involved in learning that new software, language or way of doing things. This may be particularly true for Obsidian, because it offers such an enormous amount of flexibility and customisation in its set up, requiring the user to do more than in prefab software like Notion, EverNote, Google Docs, etc.
As see in the comparisons in this article, Obsidian and Notion fundamentally share a great deal of functionality, and achieve similar goals. Both are well-supported and have large communities online, making it easy to search for help or get answers to common questions about formatting, integrations, broken features, etc. Even Notion also requires a learning curve, particularly for those who have only used very lightweight tools in the past (like EverNote, Google Keep, etc.) and are yet unfamiliar with robust note-taking software.
The up-front investment into learning a new tool is often worth it if it truly solves your problem. In this way, we argue that Obsidian is certainly not too complex and is worth learning to manage large, inter-connected and flexible knowledge systems. Our free 21-day course is the best way to get started.
Bottomline: Which is Better? Obsidian vs Notion
At the end of the day, the best note taking app for you depends heavily on your preferences and how you plan to conduct your research. Depending on your project, you may be able to immediately rule-out Notion or Obsidian based on your requirements. For example, if you’re working on classified research, require control and access to all your data, or prioritise freedom and customisation in software, you may want to go for Obsidian. If, on the other hand, you strongly prefer polished structures, easy interfaces and don’t mind some costs or dependencies as your notes grow, Notion may be the better choice.
When it comes to key the downsides, Obsidian has a steeper learning curve, and requires more up-front investment in learning how to write in Markdown and setting up the best plugins & integrations. Notion is easier to use than Obsidian, but does lock you into a system which controls your data access and could eventually require you to pay a subscription if you want to go beyond the free membership features. This is the main advantage of Obsidian over Notion: your data always remains your own and you future-proof your research for decades to come.
Although the Effortless Note Taking System for Academics is built using Obsidian, some EA members manage to create similar systems using Notion.
No matter which tool you end up using, it’s worth investing time into understanding the key features, integrations and hacks that help you really get the most out of the tool.
Learn More about Obsidian for Academics
If you are leaning towards Obsidian, then it’s easy to dive deeper with our in-depth articles and courses. The quickest way to go from A-Z on building an Obsidian-based knowledge system for research is by taking our free Note Taking Course.
You can also dive into specific questions or topics by checking out our other articles on Obsidian here:
Best Obsidian Plugins for Academics
8 Must-Know Hacks for Academic Note Taking in Obsidian
Using Obsidian Bases For Academic Note Taking
Obsidian AI Agent with the Google Gemini Scribe Plugin For Academics
Capture Any Content to Obsidian with WebClipper + AI
Connecting Zotero and Obsidian with the ZotLit Plugin + Templates
Adding AI to your Obsidian Notes with SmartConnections and CoPilot
Discovering new Ideas Hidden in Your Notes with Obsidian Bases
Styled Links In Obsidian
Organizing Big Data Collections In Obsidian
Working with PDFs in Obsidian: PDF++ Plugin and Full-Text Search
A Simple System for Long-Term Learning with Obsidian
Organizing Academic Projects with Obsidian Tags and Mind Maps
