Joplin vs Obsidian

Obsidian Sync ($4/month) provides end-to-end encryption, but it's a paid service. Users syncing via iCloud, Dropbox, or other services do not get E2E encryption of note content (the cloud provider can theoretically read your files). For free encrypted sync, users must set up third-party solutions like Syncthing or Cryptomator.

Obsidian launched an official Web Clipper extension in 2024. It supports saving web content as Markdown with customizable templates and can clip highlights, full pages, or selections. While newer than Joplin's solution, it provides solid web clipping capabilities.

Joplin supports note links but lacks true bidirectional linking, graph visualization, or block-level references. Notes can reference each other via internal links, but there is no automatic backlink detection or visual relationship mapping. Organization relies on the traditional notebook/tag model.

Joplin has approximately 300 plugins covering themes, editors, export formats and integrations. The ecosystem is healthy and growing, with a well-documented plugin API. However, the quantity and quality trail Obsidian's marketplace significantly.

Obsidian can import from Evernote via community plugins (Importer plugin), but the process requires more configuration. The organizational approach is fundamentally different, moving from notebooks to a flat file system with links requires rethinking your note structure.

Joplin stores notes as Markdown but uses a SQLite database internally with unique note IDs. Notes can be exported as Markdown or JEX format. While the Markdown is standard, the database layer adds complexity compared to pure file-based storage.

Joplin has built-in to-do functionality, notes can be flagged as to-dos with checkboxes and alarms can be set for reminders. The to-do interface is simple and functional, providing basic task management without requiring plugins.

Obsidian supports Markdown checkboxes natively. With the Tasks plugin, it becomes a capable task manager with due dates, recurring tasks and query-based task views. The built-in functionality is basic, but plugins make it capable.

Joplin provides a consistent experience across macOS, Windows, Linux, iOS and Android. The desktop apps use Electron and the mobile apps are native. The interface and feature set are well-aligned across platforms and sync keeps everything in step.

Obsidian also runs on all major platforms with a consistent experience. The mobile apps have improved significantly. With Obsidian Sync, cross-device experience is smooth. Both apps achieve good cross-platform parity.