Switch from OneNote to Joplin on Windows: Markdown, Kanban, Sync and Migration Guide

In a first-person workflow account published by How-To Geek, writer and veteran Microsoft Office specialist Tony Phillips detailed how ditching OneNote for Joplin unexpectedly reshaped his daily writing and organizational habits. What started as a digital scratchpad for research notes gradually expanded into a full drafting environment, task manager, and Kanban board.

For Windows users weighing whether to stick with Microsoft's deeply integrated digital binder or jump to an open-source, Markdown-driven alternative, this real-world workflow offers a revealing case study—complete with practical advantages, plugin tricks, and a few architectural caveats worth knowing before you migrate your own notebooks.

From Scratchpad to Drafting Studio: The Markdown Advantage​

OneNote is famous for its infinite, free-form canvas. You can click anywhere, type anything, and drag containers around like digital sticky notes. That freedom is fantastic for brainstorming, but as another recent commentary in MakeUseOf noted, many writers and technical users prefer a structured, linear document approach over an open canvas.

In Phillips's How-To Geek workflow, Joplin evolved from a place to stash research snippets into the primary editor for drafting entire articles. Because Joplin is built around Markdown—specifically following the CommonMark specification—users can structure documents on the fly using plain-text keyboard symbols for headings, bulleted lists, blockquotes, and syntax-highlighted code blocks, toggling between the raw Markdown view and the rendered rich-text preview on both desktop and mobile.

Just as importantly, leaving OneNote does not mean giving up multimedia context. Within Joplin, notes can still hold attached Word documents, embedded images, and freehand drawings right alongside the draft text. And when a rough concept graduates into an assigned deliverable, any note can be converted directly into an actionable to-do item complete with a deadline and a completion checkbox.

Bridging the CMS Gap with Plugins​

Drafting in Markdown is great until you have to paste your work into a stubborn Content Management System (CMS) that mangles plain-text formatting. To solve this, Joplin leans on a built-in plugin architecture.

By installing the Copy as HTML plugin (listed in Joplin's official GitHub plugin repository at version 1.6.6), a writer can copy rendered rich-text HTML—including headings, bulleted lists, and images—directly from the Markdown editor into a web CMS without rebuilding the document structure by hand. While CMS compatibility always depends on the target web editor you use, Joplin's official documentation also reminds users that while standard CommonMark converts cleanly to HTML, certain extra Markdown plugins enabled inside Joplin's configuration (such as Mermaid diagrams, KaTeX math expressions, or custom highlighting) are non-standard and may not render identically in external Markdown readers.

Section Summary:

• Structured Drafting: Joplin trades OneNote's free-form canvas for CommonMark Markdown with side-by-side or toggleable rich-text rendering.
• Rich Attachments: Notes still support attached Office files, images, and drawings, and can convert between standard notes and deadline-driven to-dos.
• CMS Portability: The Copy as HTML plugin bridges the gap between Markdown drafting and web publishing, though users should keep standard CommonMark boundaries in mind.

Notebooks, Tags, and Turning Headings into Kanban Boards​

How do you keep thousands of research notes from turning into a digital junk drawer? OneNote locks you into a rigid hierarchy of Notebooks, Section Groups, Sections, and Pages. Joplin takes a more flexible, multi-dimensional approach across Windows, macOS, Linux, Android, and iOS.

In the workflow described by How-To Geek, organization relies on four core pillars:

• Nested Notebooks: Creating a top-level notebook (such as "Article Research") and branching out into dedicated sub-notebooks for specific beats like Windows, Excel, and Productivity.
• Cross-Notebook Tagging: Right-clicking notes to apply existing or newly minted tags, allowing related research to be grouped logically even when the notes live in completely different notebooks.
• Full-Text Search: Using global keyword searches across all notebooks to jump quickly between results, even when multiple drafts share similar titles.
• Template Duplication: Maintaining a master template note—for instance, pre-populated with standard headings for a feature overview, Windows 10 and Windows 11 availability, and pros and cons—and duplicating it whenever a new assignment begins.

The Kanban Twist: YesYouKan​

Where Joplin really steps outside the traditional note-taking box is through community plugins that reinterpret how note data is displayed. Phillips highlighted a Kanban plugin called YesYouKan (tracked in the official Joplin plugin directory at version 1.1.3), which builds and manages visual project boards right inside the app.

In his setup, pasting an existing note's heading structure into a Kanban note automatically transformed the outline into a visual board: top-level H1 headings became board columns (To do, In progress, Done), while second-level H2 headings became individual task cards underneath them. Coupled with customizable keyboard shortcuts, that kind of modularity lets users bolt on project-management views without bloating the core app with features they never touch.

Sync, Privacy, and the Irony of Using OneDrive​

Perhaps the biggest philosophical difference between Microsoft OneNote and Joplin is how they treat your storage. OneNote is fundamentally cloud-first, tightly bound to OneDrive and your Microsoft account. Joplin, according to its official documentation, is explicitly offline-first: your notes live locally on your PC or phone first, ensuring full access whether or not you have an internet connection.

When you want cross-device synchronization—say, checking off a task list on an iPhone and seeing that status reflected on a Windows desktop—Joplin uses an abstract sync driver architecture designed to avoid vendor lock-in. Out of the box, Joplin supports syncing via:

• OneDrive
• Dropbox
• Nextcloud
• WebDAV and S3
• Local filesystem (useful for network drives or third-party folder sync tools)
• Joplin Cloud (a paid first-party option that previous How-To Geek coverage priced at $4/month for Basic, $7/month for Pro, and $9.50/month for Teams)

There is an undeniable bit of irony in ditching OneNote to reduce reliance on Microsoft 365 while still choosing Microsoft OneDrive as Joplin's sync backend—the exact route Phillips took for his desktop-to-iPhone setup. However, Joplin's official OneDrive documentation points out an important architectural boundary: when connected to OneDrive, Joplin creates an isolated subdirectory at /Apps/Joplin and reads and writes exclusively within that folder. The application has no access to any other files in your OneDrive account.

Two Critical Sync and Encryption Rules​

If you are setting up Joplin across multiple devices for the first time, the official Joplin documentation outlines two critical operational caveats that casual walkthroughs often gloss over:

• Let the Initial Upload Finish First: When moving an existing note collection into Joplin on your primary PC, you must wait for the first synchronization upload to finish completely—monitoring the progress indicator in the left sidebar—before connecting any secondary phones or laptops. Connecting a second device mid-upload can result in incomplete data appearing initially.
• Enable End-to-End Encryption (E2EE) on One Device Only: While privacy advocates on WindowsForum and MakeUseOf rightly praise Joplin's End-to-End Encryption, E2EE is optional and must be enabled manually. Joplin's documentation warns that you must enable E2EE on a single device first (ideally a desktop PC, which encrypts large attachment libraries faster than a phone), set a Master Key password (which cannot be recovered if lost), and let that encrypted sync finish completely. Only then should you sync your secondary devices so they inherit the same master key. Enabling E2EE on multiple devices simultaneously will generate conflicting encryption keys.

How to Actually Move Your Data from OneNote to Joplin​

The biggest hurdle to leaving OneNote used to be getting your data out in one piece. Historically, users had to bounce their notebooks through Evernote's .enex format or third-party scripts. Today, however, Joplin's official import/export documentation details direct native import paths for OneNote—provided you are running a recent version of Joplin on Windows and understand the version boundaries.

Step-by-Step: Importing from the OneNote Windows Desktop App​

If you use the standard OneNote desktop client on Windows, here is the officially documented procedure to migrate your notebooks into Joplin v3.5.5 or newer:

• Open the OneNote desktop application on your Windows PC.
• Click File > Export.
• Choose either Section and select OneNote 2010–2016 Section (*.one/*.onex), or choose Notebook and select *OneNote Package (`.onepkg`)**. Save the file locally.
• Open the Joplin desktop application on Windows.
• Navigate to File > Import > ZIP - OneNote Notebook and select the file you just exported from OneNote.

(Note: If you are migrating from OneNote Online instead, open OneNote Web, click "Show all notebooks" to open OneDrive, locate the notebook folder under "My Files," right-click to download it as a .zip backup, and import that .zip using the same File > Import > ZIP - OneNote Notebook menu in Joplin.)

Keep in mind that complex OneNote layouts—especially heavy freehand ink and massive attachments—have required ongoing refinement. Joplin's desktop changelog for version 3.6.11 (released in May 2026) specifically noted fixes for OneNote ink-import errors, timestamp preservation, special characters in note titles, and large attachments. Always keep your original OneNote files intact until you have verified that every section imported cleanly.

True Data Portability Going Forward​

Once your workflow lives inside Joplin, you are never trapped inside a proprietary database again. As both How-To Geek and Joplin's documentation confirm, you can export single notes, individual notebooks, or your entire library into HTML, PDF, plain Markdown, Markdown with front matter, or Joplin's native JEX (a lossless .tar archive that preserves all notes, attachments, tags, geolocation, and timestamps) and RAW directory formats.

Does Joplin completely replace the polished ribbon UI of Microsoft OneNote or the sheer value of the 100GB OneDrive storage bundled with a $19.99/year Microsoft 365 Basic plan, as outlets like XDA and PCMag have pointed out in their platform comparisons? Not for everyone—especially if you live by a stylus and an infinite whiteboard.

But if your daily work revolves around structured writing, organized research, portable Markdown files, and a workspace that bends to your habits through open-source plugins, Joplin proves that a humble note-taking app can quietly take over your entire workflow—in the best possible way.

Correction (October 18, 2026): The migration table originally said .onepkg imports only work when Joplin is running on Windows. Joplin v3.6 added .onepkg import support on Linux and macOS, so the table has been updated to reflect that the Windows restriction applies only to the OneNote desktop export step. Source: Joplin desktop changelog (joplinapp.org/help/about/changelog/desktop/).