Obsidian vs OneNote for Academic Work

With the stellar rise of tools like Obsidian, millions of students and academics rocking “traditional” apps like Microsoft OneNote are wondering whether the time has come for a switch. Today, we compare the two with an eye for the Obsidian beginner — addressing common pain points of Obsidian coming from a OneNote user perspective.

Before we begin, it is safe to say both tools can handle basic note-taking perfectly well. Their real benefits and disadvantages only become visible by compound: when your collection grows to hundreds or thousands of notes, survives for years, or starts supporting more complex workflows involving project-management and automation.

At that point, as we will see, OneNote and Obsidian start to drift apart.

What is Obsidian?

Obsidian is a note-taking app whose main advertised feature is that of linking your notes into a web of interconnected ideas. As an academic, even if you never tried Obsidian, you have probably seen a picture like this before:

This is Obsidian’s Graph View: the dots are notes, and the lines represent links between those notes. For an analogy on why this is interesting, think of Wikipedia. Wikipedia is nothing but a giant web of articles mentioning each other. The article on hydrogen mentions the Sun, the Sun article mentions the Solar System, which in turn mentions Neptune, which mentions the mythological Roman god with the same name, and so on and so forth. You get the idea.

Obsidian notes are stored in a vault, which is really just a folder in your computer. They can be organised in various ways depending on your specific needs: Obsidian has a fairly rich “core” set of functionalities, but many plugins can be installed to extend it and make it truly yours. We will cover these aspects below.

If you want to know more about the fundamentals of Obsidian — how to install it and start using it right away — check out this blogpost:

What is OneNote?

OneNote is a note-taking app part of the Microsoft Office Suite (though it is available as a free standalone app). OneNote takes a much more traditional and familiar approach to note-taking. Notes are organised into notebooks, which contain sections, which in turn contain pages. The metaphor with physical organisation is obvious, and is basically identical to how users commonly explore digital files (in a folder structure).

OneNote looks and acts very much like an old-school Microsoft Office product (the first version of OneNote came out all the way back in 2003). If you are used to MS Word, the feel is similar. OneNote pages themselves are unusually free-form however. You can move content around and scribble on the page. This makes OneNote feel natural for taking notes during lectures, meetings, and brainstorming sessions.

Obsidian vs OneNote Features Comparison

File format

Obsidian stores notes as .md markdown files on your computer you can open and read yourself with any text editor. OneNote uses its own format .one.

The difference in file format might seem like a minor technical detail now. But having your notes as plain Markdown can prove very valuable if you decide to move to another app in the future. It is also a much friendlier format for LLMs to parse if you plan to use AI.

File ownership

An Obsidian vault is a folder on your computer containing markdown files (the notes) and attachments (like images and PDFs). You decide where that folder lives, and whether it is synced through Obsidian Sync — their official cloud service — or any other cloud solution you might be using, like iCloud, OneDrive, Git, etcetera.

OneNote stores notes locally on your device and syncs them via Microsoft OneDrive, but you cannot access the files directly outside the app.

Though having to decide how to sync your notes might seem like an unnecessary step. Having total, fine-grained access to your note collection down to the individual files is important if you expect it to survive in the long term. It is way easier with Obsidian to move your notes, read them through other apps, feed them to AI, and manipulate them in various ways just like any other file on your computer.

Folders & Links

Despite Obsidian being renowned for its note-linking feature, both apps can link notes together. OneNote supports links to notebooks, sections, pages, and even individual paragraphs. Obsidian, however, brings linking to a different level through backlinks and graph views.

Both apps also have folders. OneNote enforces the Notebook → Section → Page folder hierarchy. Obsidian, instead, does not care how you organise your folders, and puts more emphasis on links and custom organisation built with tags and properties (next section).

OneNote gives you structure immediately, but only ever gives you one structure. Obsidian allows for multiple navigation systems to emerge from what you are actually doing, but doesn’t necessarily enforce any. This can either be a blessing or a curse, depending on the practices you establish (see the pain point below Navigation).

Tags, properties and collections

The two tools differ sharply here. OneNote supports tags that attach to individual elements on the page. There are built-in tags like “To do” and custom tags as well. Tagged content can then be searched across your notebooks. Obsidian supports tags as well. They can be inserted directly by adding an hashtag (#), and can be nested too with a slash / (for example, #books/unread)

Obsidian, however, also supports properties. Properties let you attach arbitrary metadata to enrich a note with custom types such as authors, dates, topics, status or project names. You can then collect, filter, sort and display notes by tags and properties, using the Obsidian bases feature.

As your notes become more dispersed, being able to retrieve them, sort them and display them in meaningful ways becomes increasingly valuable. Whilst OneNote provides a good tag system, Obsidian gives you the pieces to create a refined knowledge management system.

Writing and free-form notes

On this end, OneNote has a marked advantage when annotating with some kind of stylus. Its pages behave more like paper than text documents. You can draw and annotate diagrams, mix handwriting with typed text and assemble elements freely. This can be great for a student annotating a lecture on her tablet.

Obsidian is fundamentally text-first and can feel rigid and more document-like in comparison. Obsidian’s Canvas feature somewhat bridges the gap, allowing users to place cards and images freely on a canvas, but does not quite match the same natural feel of OneNote.

This point is quite subjective, as it depends a lot on how you take notes, and when. The rigidity of markdown can be annoying during fast-paced note-taking in a class or meeting. During study and research though, priorities usually shift considerably.

Customisation and plugins

OneNote supports what Microsoft calls add-ins (ie. plugins) and integrations on paper, but suffers from a very thin community that only maintains a handful of active plugins. Microsoft gives OneNote useful connections to Outlook, Teams and automation tools. But the ecosystem is small, fragmented and heavily Windows-centric.

On the contrary, Obsidian is famous for its vast collection of plugins that enhance and extend the app in almost every way. Whilst OneNote is essentially a finished product, Obsidian is closer to a blank canvas that can adapt much more radically to your needs and workflow.

Down the road, Obsidian’s pliability makes it a powerful choice for academics and professionals to build custom workflows. It isn’t all sunshine and rainbows though, plugins can become a complexity barrier for Obsidian newcomers (see the pain point below Plugins).

Reference Management

For academics, Obsidian has a considerable advantage when working with reference managers such as Zotero. Community plugins can search your Zotero library, insert citations, import literature notes and even pull PDF annotations directly into Obsidian. OneNote has no comparable Zotero integration ecosystem, so references generally have to be copied, linked or manually managed alongside OneNote rather than from within it.

This becomes increasingly valuable as your research library grows and you begin building more structured literature-review workflows around your notes.

Formatting

OneNote offers a more immediate WYSIWYG (what you see is what you get) editing experience, with fonts, colours, highlighting, tables and freely positioned elements available from the start (like in other MS Office applications). Obsidian’s Markdown means formatting is deliberately simpler and largely text-based. If you want a more familiar formatting toolbar, you will usually need plugins such as Editing Toolbar or cMenu.

Coming from OneNote, this can feel restrictive. As your note collection grows, however, Markdown’s simpler formatting can become an advantage: it keeps notes lightweight, consistent and readable outside Obsidian. If you wish for or need elaborate styling, you can still achieve it via themes, CSS and plugins.

Obsidian OneNote Import

The easiest way to move a OneNote collection into Obsidian is the official Importer plugin for Obsidian. There are two ways you can import OneNote notebooks into Obsidian:

1. by connecting the Importer to your Microsoft OneDrive account and importing the synced notebooks.
2. by directly importing OneNote files (.one and .onepkg) locally saved on your computer.

Obsidian OneNote Import Not Working

There are some well-known issues related to the Microsoft OneDrive import process (method 1 from above):

Import is taking too long → Microsoft throttles the transfer speed; there is unfortunately no workaround for this. Some large notebook imports may take a while.

My notebooks do not appear for import → This method only works with notebooks that are synced with your OneDrive account. To check which notebooks are synced, open to the web version of OneNote here, and check the notebooks available.

Some of my OneNote notebooks are not being exported → this is usually due to two reasons: (1) password-protected sections are skipped, make sure to remove the passwords from OneNote before importing into Obsidian; (2) only notebooks owned by your account can be imported. Shared notebooks cannot currently be imported with this method, and work or school accounts may require organisation approval.

Imported notes are empty or missing content → This can happen for notes you access rarely. The easiest fix is to use method 2, explained in the next section.

My notes don’t look the same once imported → Due to inherent differences in how OneNote and Obsidian format their files, your notes will likely not look the same (cf. the features comparison section for details). However, you should be able to import all the content, even hand-drawn elements, into Obsidian.

Importing OneNote notebooks in Obsidian from local files

Most of the issues mentioned can be avoided by using the local import method. It is slightly less automated, but worth it if you are having troubles with the OneDrive method. This way works on both Mac and Windows (some methods explained online only work with the Windows app).

First, get Obsidian ready on the side. Make sure to install the Importer plugin. Then open Obsidian Settings (Ctrl,or ⌘,) > Importer > Microsoft OneNote > File Import. This will land you on a tab where you can drag and drop OneNote files.

Open the OneNote application (not the browser version) on your Mac or Windows computer. Go to Settings (Preferences) > Backups. Then click on Back Up All Notebooks Now, This will save the latest versions of your notes locally. In the same tab, access the backed-up files by clicking on Open Backup Folder. This will open the file explorer to the location of OneNote’s backup folder, look inside the folder and grab the .one files you need (you can temporarily copy them to a folder on your desktop if you wish).

Finally, drag and drop those files into the Obsidian Importer tab we opened initially. From there, just follow along a quick import process.

If you need further guidance, check out Obsidian’s dedicated page for importing from OneNote.

The Pain Points of Obsidian

Obsidian’s perceived difficulty — compared to a simpler tool like OneNote — tends to originate from three places: navigating/organising your notes, choosing the right plugins, and developing a practical method for using them.

Obsidian Navigation & Organisation

OneNote gives you a folder-like system and some tags. Obsidian leaves you to figure out how and when to use its organisation features. Indeed, you can choose to organise your Obsidian vault to mimic a simple folder system like OneNote, or you can go all-out with notes linking, bases, tags and properties.

Again, the real benefits of choosing one organisation vs another become visible once your collection grows to a considerable size. Folders enforce a hierarchy that makes navigation familiar, but often a note might belong to multiple domains and relate with distant concepts in a way that folders just cannot capture. On the other hand, graphs become hard to navigate quickly, unless you take precautionary steps.

👉 To learn more about these concepts, and exactly how to implement advanced solutions to common Obsidian pain points, check out the Information Management Course. It is a structured, hands-on journey up Obsidian’s learning curve. A section is dedicated precisely to organisation, an absolute essential for working with Obsidian at scale.

Obsidian Plugins

Plugins are Obsidian’s greatest strength but also a potential barrier to entry. There is an ocean of tools and the freedom to fish out whatever you want from it. It is therefore common to run into these sorts of issues:

1. Installing plugins which conflict in more or less subtle or destructive ways.
2. Installing old and no longer maintained plugins, which have been surpassed by better alternatives you don’t know about.
3. Simply installing too many plugins and not using most of them, thus polluting your workspace to no benefit.
4. Wasting hours setting things up and trying to understand how each plugin works, before writing a single note.

There is huge allure in Obsidian’s extensibility, but too much freedom often works squarely against the real goals of academics (writing that paper, doing that lit review, reading through those PDFs, …). This is always the case, but is especially true if you are an Obsidian beginner. Some hints to mitigate these risks:

1. Aim for the smallest set of plugins that achieves the goal.
2. Avoid plugins no longer actively maintained.
3. Look for curated collections of plugins, depending on your use case.

In previous posts, we explored many useful Obsidian plugins for academics, feel free to check these out:

👉 The Information Management Course goes through the installation, customisation and detailed explanation of an expertly curated list of plugins to supercharge your Obsidian for academic use. You will not only install plugins that work together, but that work off each other to enhance your note-taking experience.

What Makes Obsidian More Effective Than OneNote?

Obsidian can be more effective than OneNote for academic work because, when used in conjuction with a solid workflow, it lets you separate different pieces of knowledge and connect them across domains, projects and contexts. OneNote is excellent for quickly capturing information in a familiar, paper-like manner.

OneNote often encourages monolithic notes: a single lecture page might contain the lesson’s main points, questions, ideas, summaries, references and links. These pieces remain tied to the original page, making them easy to overlook and difficult to reuse elsewhere. In Obsidian, a question, concept, author or research idea can become its own note and connect to courses, projects and related topics.

Obsidian can help tremendously when looking for novel relationships during research, managing big projects, and organising work that spans years and even decades. However, Obsidian will not create these connections for you. No graph view or set of plugins will be a substitute for thinking, and simply installing the app will not make you a more productive or creative academic. To use Obsidian effectively, you need a method: you must decide what deserves its own note (and what kind of note it should be), how ideas should be linked and how your notes should be reviewed over time.

Coming up with a method, implementing it, testing it, and improving it, is neither easy nor quick. And that’s the main reason why Obsidian feels like a steep climb for many.

👉 I recently posted a free, almost hour-long youtube video explaining the fundamentals of Obsidian for academics. This can greatly help newcomers start developing their very own workflow. Give it a watch if you can:

Summary

OneNote and Obsidian are both capable note-taking tools with valid use cases, but they optimise for very different experiences.

The verdict: choose OneNote if you mainly want a straightforward digital notebook for meetings and lectures. Choose Obsidian if you want a flexible knowledge system that can grow with your research and academic work.

Want to use Obsidian but unsure where to start? The Effortless Academic 21-Day Course guides you through building that coveted Obsidian workflow, so you can spend less time figuring out your system, and more time on actual academic work.