OneNote vs Joplin on Windows: Markdown, Plugins, Performance and Notebook Migration

For anyone managing years of personal documentation or enterprise project notes on a Windows PC, that distinction matters. Choosing between OneNote and Joplin is less about picking a "better" program and more about deciding whether your brain works best on an infinite digital whiteboard or inside a disciplined, linear text editor.

The Double-Edged Sword of OneNote’s Infinite Canvas​

Microsoft designed OneNote—across OneNote for Microsoft 365, OneNote 2024, OneNote 2021, and OneNote 2016—around the concept of a free-form digital notebook. According to Microsoft Support documentation, users can click anywhere on a virtually endless scrolling page to spawn independent note containers. Those boxes can hold typed text, web clippings, images, audio, video clips, and digital ink, and they can be dragged into whatever spatial arrangement suits the moment.

On a wide desktop monitor or a Surface tablet with a stylus, that spatial freedom feels liberating. You can place a checklist next to a diagram, tuck a side thought into the margin, and treat the screen like a physical desk.

However, Bamisile highlights the hidden trap of having no guardrails: without an enforced layout, a page can quickly devolve into a cluttered patchwork of scattered text boxes. Worse, spatial layouts built on a laptop or tablet frequently fall apart when opened on a smartphone screen, where side-by-side containers no longer fit the viewport cleanly.

Joplin approaches note-taking from the opposite philosophy:

• Linear, Markdown-first structure: Joplin stores notes in plain-text Markdown following the CommonMark specification, encouraging users to rely on standard headings, bulleted lists, and checkboxes rather than arbitrary screen coordinates.
• Predictable cross-device reading: Because Markdown flows top-to-bottom rather than side-to-side, notes maintain a consistent structural hierarchy whether viewed on a Windows desktop, a mobile app, or even a terminal client.
• Built-in technical extras: Per Joplin's official documentation, its Markdown engine also supports KaTeX math notation, mhchem chemical equations, Mermaid diagrams, and even ABC musical notation out of the box.

That said, Markdown is not a magic wand without compromises. While Joplin includes a WYSIWYG Rich Text editor for users who dislike seeing raw formatting symbols like asterisks and hashes, Joplin's documentation warns that notes remain Markdown under the hood. Switching a complex note into Joplin's Rich Text editor can strip out special formatting from non-fenced Markdown plugins, force empty headers onto tables, and reject mixed list types (such as combining standard bullets and checkboxes in a single list). If your workflow relies on freehand drawing, arbitrary side-by-side callouts, or complex multimedia layouts, OneNote's spatial canvas remains purpose-built for that job.

Section Summary: OneNote excels as a spatial, multimedia canvas for visual thinkers and pen users, while Joplin enforces a clean, top-to-bottom Markdown structure that prevents layout clutter across different screen sizes—provided you accept the formatting rules of Markdown.

Extensibility and Customization: Plugins vs. Fixed Suites​

Another major dividing line is how much control the user has over the software's interface and capabilities. OneNote is tightly woven into the Microsoft 365 ecosystem, offering dependable built-in tools like note tags (Important, To Do), instant Alt+Shift+D date stamps, and seamless links across notebook sections. What it does not offer is a community-driven modding scene or deep visual theming beyond Microsoft's preset options.

In MakeUseOf's account, Bamisile noted that while Joplin does not require add-ons to function well, its community plugin repository makes it easy to bolt on Kanban boards or enhanced backlinks between notes, alongside custom CSS for deeper interface personalization.

Based on Joplin’s official help documentation, Windows power users looking to customize their setup should keep several practical details in mind:

• Installing and managing plugins: Both the desktop and mobile versions of Joplin support plugins via the Configuration screen's Plugins page, either by searching the built-in repository or manually loading a Joplin Plugin Archive (*.jpl) file. Vetted plugins carry a gold crown icon. Toggling or installing a plugin requires fully restarting the application—making sure it exits completely rather than just minimizing to the Windows system tray.
• Platform restrictions: While Windows and Android allow broad plugin installation, Apple App Store guidelines restrict the iOS version of Joplin to installing only "recommended" plugins.
• The reality of Custom CSS: Joplin allows users to restyle rendered Markdown via userstyle.css and overhaul the application interface itself via userchrome.css inside the user profile directory. However, the Joplin development team explicitly cautions that these are advanced settings; because the team does not guarantee a stable underlying HTML structure across updates, custom stylesheets can break from one release to the next and may require ongoing maintenance (as well as careful testing to ensure dark-mode styles do not ruin printed notes).

Section Summary: Joplin gives tinkerers a rich playground of community plugins and CSS overrides that OneNote cannot match, though users must manage app restarts, iOS plugin limits, and potential stylesheet breakage after updates.

Resource Usage and Application Weight​

Performance is often the final straw for long-time OneNote users. Because OneNote carries the weight of Microsoft 365 integrations and a complex spatial rendering engine, it can feel heavy. In his MakeUseOf piece, Bamisile reported experiencing slowdowns and occasional crashes when working with large OneNote notebooks or heavy attachments, observing OneNote consuming roughly 1 GB of RAM on his machine while Joplin stayed under 300 MB and rarely lagged.

From an engineering perspective, it is important to treat those specific memory numbers as one writer's personal observation rather than a universal benchmark, since RAM consumption varies dramatically depending on hardware specs, notebook size, embedded attachments, and background sync state. Still, the underlying architectural contrast is real: parsing plain-text Markdown files locally requires far less overhead than rendering an infinite 2D canvas populated with rich media containers.

Furthermore, moving to Joplin does not actually require abandoning Microsoft's cloud storage if you already pay for it. According to Joplin's synchronization documentation, while the app is local-first, it natively supports syncing across Joplin Cloud, Nextcloud, S3, WebDAV, Dropbox, the local filesystem, and Microsoft OneDrive.

Section Summary: While exact memory footprints depend on your PC and workload, Joplin's plain-text architecture feels noticeably leaner than OneNote's suite-heavy canvas, and it still lets Windows users sync through OneDrive if they choose.

How to Migrate Your Notebooks from OneNote to Joplin​

If you are tempted to test whether a linear Markdown workflow cures your disorganized notes, you no longer have to copy and paste pages by hand. Joplin's official import documentation outlines two direct migration paths for OneNote users, depending on which version of OneNote and Joplin you run.

Method 1: Importing from OneNote Online (Joplin 3.5.1 or later)​

This method works for notebooks stored on OneDrive, though Joplin notes it may fail on massive notebooks exceeding 2 to 4 GB:

1. Open OneNote Web in your browser and click Show all notebooks to jump to your OneDrive storage.
2. In OneDrive, navigate to My Files, locate the folder holding your OneNote notebooks, right-click it, and select Download to save a ZIP backup to your PC.
3. Open the Joplin desktop application (version 3.5.1 or newer) and click File > Import > ZIP - OneNote Notebook, then select the downloaded ZIP archive.

Method 2: Importing from the OneNote Windows Desktop App (Joplin 3.5.5 or later)​

If you use the traditional OneNote Windows desktop application (not the legacy "OneNote for Windows 10" app), you can export directly from the client:

1. Open the OneNote desktop app on Windows and go to File > Export.
2. Choose Section and select OneNote 2010–2016 Section (*.one/*.onex), or choose Notebook and select *OneNote Package (`.onepkg)**. *(Note:.onepkg` files can only be imported when running Joplin on Windows.)
3. Open the Joplin desktop application (version 3.5.5 or newer), navigate to File > Import > ZIP - OneNote Notebook, and select your exported .one, .onex, or .onepkg file.

Whether you stick with OneNote for its unmatched digital inking and spatial freedom or jump to Joplin for the structured calm of Markdown, the best note-taking app on Windows is ultimately the one that keeps your thoughts easy to find six months after you type them.