When comparing Microsoft OneNote vs Joplin, the Slant community recommends Joplin for most people. In the question“What are the best cross-platform task apps?” Joplin is ranked 5th while Microsoft OneNote is ranked 37th.
Specs
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Pros
Pro Text can be added anywhere like a whiteboard
OneNote allows you to arrange text freely on the digital paper mimicking the way it would be done with a real pen on real paper.
Pro Comprehensive organization methods
Can have multiple 'sections/tabs' at the top like in a web browser with many notes within each 'section/tab'. Also, there can be sections within section groups infinitely. The complete hierarchy looks like this: Notebooks > Section Groups ... Section Groups > Sections > Pages > Sub-pages > Sub-pages.
Pro Supports hierarchical organization of information / notes
OneNote is designed to allow hierarchical organization of information. This is achieved with grouping into the following categories and UI elements (Notebooks, Sections, and Pages). Both Sections and Pages allow additional groupings that can be expanded / collapsed in list view.
This can be incredibly helpful for quickly taking notes and organizing them for work or personal projects.
For example, you could have a Notebook for "Cooking Recipes", with sections for "breakfast, dinner, desserts", where individual recipes would be page entries (i.e. the "Desserts" section would have pages for brownies, chocolate cheesecake etc).
Pro Powerful table editor
Adding and resizing rows and columns is easy and flexible. This makes for an easy way to adjust a note as it grows in content size.
Pro Insert files into your notes
You can add a variety of different files into your notes including images, video, audio, and more.
Pro Strong search features let you quickly find what you're looking for
If you don't want to search through all of your notes, you can narrow it down by specifying the page, section, group, or notebook.
You're not limited to just searching through your text either. You can search for text in images, video recordings, and audio (this is off by default).
Pro All indented lines under the first can be expanded and hidden
Which makes it easy to quickly look at the high level of notes, and then drill deep into each point.
Pro Add notes through email
You can choose what notebook the notes will save to. E-mail notes to your special Onenote e-mail and it will be accessible across all devices.
Pro Stylus and digitizer pen support
OneNote can be used on all touch capable devices via stylus or digitizer pen making for an intuitive and easy way to take notes by hand, which can often be faster or just preferred over typing. It has the best pen input out of any note taking app.
Pro Very similar design for those used to Microsoft programs
If you have experience with other Microsoft programs such as Microsoft Office, you'll feel right at home with the design of OneNote thanks to the similarity of the menus.
Pro Lots of options for customizing fonts
You can fully customize your default font (the color, type of font, and font size). You can override this styles with the same options (and more) in individual notes.
Pro Converts handwriting to text on Windows version
You can take handwritten notes on your mobile device with a stylus or digital pen and then convert the handwriting to text later on your Windows PC.
Pro Article Web Clipper available on desktop and mobile
Has a web clipper extension on Chrome and Edge that can be used for clipping whole articles and images. Web clipping of articles is also available on Chrome mobile through the "Share" option.
Pro Cross-platform
Its available Windows Mobile, Windows Store, Android, a Desktop Version, and a Web app. Apple macOS and iOS are also supported.
Pro Table is sortable
Pro Integrates with other Microsoft services
Integrates well with Outlook, Office, and OneDrive.
Pro Sharing and collaboration
You can share your notes by inviting people with an e-mail, or by giving them a direct URL. You have control over what kind of access the user has on your note (read only, edit) and can revoke it at any time.
OneNote will alert you when a chance is made on your shared note.
Pro Offers flexible encryption
Unlike most other apps, you can selectively password protect, and fully encrypt, individual documents or entire folders. This is especially important to many people with data stored in the cloud. As of early this year, even the free version supports encryption. Microsoft has also enhanced their internal security methods for storing data on OneDrive (where OneNote performs sync), which makes it more secure than most of their competitors (including Evernote).
Pro Mathematical calculations
You can perform mathematical calculations in OneNote like a calculator.
e.g. 1+2=3,
85/4=21.25,
8!=40,320,
7^2=49
Pro Ink to Math
Handwritten mathematical equations can be converted to typed mathematical equations. Moreover, you can ask OneNote to solve the equation too.
Pro Optical character recognition
You can copy / search text in images added to OneNote.
Pro Page versioning
You can view the history of any page and revert to a previous version.
Pro On Android, you can tap a badge to start a note
The badge on Android hovers over on your screen similar to Facebook Messenger's Chat Heads. You can tap it and instantly start jotting down your thoughts without having to flip to the app first.
Pro Import and link calendar events and tasks in Outlook
This is great for taking meeting minutes. You can import all the meeting details, including a checklist of attendees and a link back to the original event in your Outlook calendar. You can tag all the actions coming out of a meeting and you can create linked tasks from them in Outlook. Much quicker and more effective than writing meeting minutes the traditional way.
Pro Browser plugins allow easy saving of web pages
The ability to quickly file away web clippings is a key part of note taking.
Pro Large variety of themes available
You have quite a few options for themes available with illustrated backgrounds. If you want something a bit more simple while still having personality, there are also several color themes.
Pro Offline access
Pro Open source
Peace of mind that there is no malicious piece of software in the app.
Pro Encryption
Pro Cross-platform
Supports Windows, Mac, Linux, Android and iOS.
Pro Supports file attachments
Pro Supports markdown
Pro Supports tags for notes
Pro Web Clipper
Browser extension saves full pages, clean content, or screen selections to new notes.
Pro Optional CLI interface
Provides a CLI interface for terminal lovers.
Pro Supports multiple languages
English, French, and Spanish, Italian, German, Czech and many others.
Pro Active user forum with support from app creators
Support, troubleshooting, and new feature requests are easy to make at the user forum and you can contact the app creator directly.
Pro Dropbox support
Can sync using Dropbox.
Pro Nextcloud support
Pro Timed alarm reminder for to-do lists
Cons
Con Not available for Linux
There is no native Linux client for OneNote available, and most likely will never be created. Users can use the web based client, but a native app would be a better choice for those that use the app frequently.
Con Requires a Microsoft account
You need to have a Microsoft email to sign up for OneNote (Outlook, Hotmail, or Windows Live).
Con Not open-source
This application is proprietary, and thus cannot be modified or freely distributed.
Con The added flexibility means your notes may feel cluttered
Since you can place elements anywhere you'd like on your note, you have to pay attention to how you structure it. For some this added flexibility is a huge selling point, but for others it could become distracting and makes notes feel difficult to digest.
Con Menu/ribbon can feel crammed
OneNote offers a lot of formatting options, which results in a lot of options being crammed into the ribbon. It can feel somewhat cluttered and takes a bit of time to get used to.
Con Sync isn't stable
Many users have reported synchronization issues. While not everyone will experience this, it can be difficult to troubleshoot, with some fixes resorting to editing registry keys in Windows when using the Windows client.
Con Text editing is weird (poor UX)
When clicking in the middle of a note, it adds something like a text-box positioned in the middle. If you move that field to the bottom right, it gets weirder. You can end-up with an empty note, having an empty text-box 1km to the bottom-right of it.
Con Syncing issues
It tells you there are conflicts between a note on the PC and on the Android because of the timing of the synchronization but doesn't try to resolve itself.
Con Platform dependent
The newer versions for Windows and Mac are converging, using the Windows style layout (with a more more consistent and usable UI).
The original OneNote for Mac for example is very different from OneNote for Windows. Because Microsoft has a vested interest in making sure the Windows version is superior, the Mac version tends to lag behind in terms of functionality. Tutorials and other forms of documentation available online generally apply only to the Windows version, which implies non-Windows versions are undocumented.
Even worse, because the documentation rarely, if ever, indicates it only applies to Windows, it's easy to waste hours trying to make non-existent features work. As such, the documentation is "negative documentation" (i.e. worse than no documentation at all).
Con Doesn't automatically sort (by name, size, date)
You can't choose to sort automatically. Just do it manually.
Con No backup on Windows 10 free version
If you accidentally delete a section on the windows 10 free version of Onenote, there is no backup to fall back on.
Con Search function is lacking advanced features
e.g. Searching for "friend" will find "friendship" and "friendly" (because "friend" is at the beginning of the word); using this query will not find words such as "girlfriend" or "boyfriend."
Con Uninspired, bland user interface
Many of OneNote's competitors use Material Design and bold colors to create a minimal, clean looking interface.
OneNote has a bit more of an outdated look and can feel over crowded at times.
Con Annotations can’t be anchored to a photo
If you annotate a photo or some text, then insert some text above it, the annotations don’t necessarily move with the photo and get misplaced.
Con iPad version is behind the Windows version in features
Biggest issue for me is that you’re stuck with the default, example tags - you can’t import custom tags from your Windows copy, or create and delete tags.
Con Some features require external apps
Sort pages, find and replace, etc need external apps called onestatics.
Con You cannot use local OneNote files with the version of OneNote that is included with Windows
There is a difference between the OneNote that is included with Windows 10 and the OneNote that comes with Microsoft Office. The version included with Windows cannot use local OneNote files and requires you to be online to access your notes.
See here for this and other differences.
Con Sync issues with Android
If update on Linux then sync on Android, sometimes the Android sync will duplicate or remove some journal notes. Seems to be a bug in the Android app. The Linux app alone without sync with Android seems to work well using Dropbox. But don't expect changes you make on Android to sync properly back to Linux.
Con Sync issue under Linux
The Linux client has a bug that requires the user to click the mouse frequently in order for sync to proceed. This bug has been open for a while.
Con Gargantuan memory footprint
1GB+ of memory for taking notes.
Con Old school interface
Con Bloated
This project is suffering from feature creep and uses a lot of memory for a note-taking app.
Con App Image launches very slowly
On Linux, you can only install via App Image, which take 5+ seconds to launch. I can launch LibreOffice in under two seconds.
Con Sync issues on Windows
No way to change account settings and sync easily corrupted.
Con Weak tag searching
Joplin can currently only search for a single tag at a time. None of the boolean operators (AND, OR, NOT) are available for use in searches. This greatly diminishes the usefulness of tags in Joplin.