Switching from Obsidian to Joplin: Open, offline-first knowledge management

The day-to-day grind of maintaining a sprawling Obsidian vault finally pushed one user to try a different path: they migrated thousands of notes into Joplin, and within weeks declared they weren’t going back — praising Joplin’s genuinely open-source model, straightforward sync options, and noticeably lower maintenance overhead.
This move — from a file-per-note, plugin-heavy second brain to an app built around an offline-first database and pragmatic syncing — is an instructive case study for anyone wrestling with knowledge‑management fatigue. The switch highlights a recurring tradeoff: flexible, extensible platforms that reward setup and tinkering versus simpler, reliable tools that let you capture, find, and act on information without constant babysitting. What follows is a detailed, technical, and practical examination of that migration: why Joplin works for this user, where Obsidian still shines, and what risks and realities power users should evaluate before switching note platforms.

Background / Overview​

Obsidian and Joplin occupy similar territory — modern, markdown-based note apps used for personal knowledge management — but they take very different design approaches.

• Obsidian is a local‑files model (a vault composed of markdown files) with an extensive plugin ecosystem and powerful visualization tools such as the global graph. Its optional first‑party sync and publish services are paid add-ons. (obsidian.md)
• Joplin is an offline‑first notes and to‑do app that stores notes in an application-managed database (with full markdown support), provides an official Web Clipper, supports multiple sync backends (Nextcloud, Dropbox, WebDAV, OneDrive, Syncthing, and its own Joplin Cloud), and offers export/import formats (including .jex). It is free and open source. (joplinapp.org, github.com)

The MakeUseOf user’s account underlines three practical friction points that drove the migration: subscriptions and sync limitations, performance and scale, and an excessive time sink spent on maintenance rather than productivity.

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Why the switch made sense: practical drivers​

1) Subscription friction vs. open‑source choices​

Obsidian’s core app is free and fully functional for offline use, but the official Obsidian Sync service — marketed as a seamless, end‑to‑end encrypted sync and version history solution — is a paid add‑on (the standard sync plan is a paid subscription). For users who want a frictionless first‑party sync across devices, that introduces recurring cost and limits (storage caps, revision history tiers). (obsidian.md)
By contrast, Joplin lets you keep a free, self‑managed sync setup using cloud storage you already use (Nextcloud, Dropbox, OneDrive, WebDAV) or peer‑to‑peer tools (Syncthing), and it supports encryption for the sync layer as an optional feature. That removes a recurring cost and gives users direct control over where their encrypted sync blobs live. (joplinapp.org, github.com)
Caveat and verification: Obsidian still allows users to sync by using third‑party cloud folders (e.g., Dropbox) because the vault is just a folder of markdown files. The distinction is that Obsidian’s built‑in sync convenience and extra features (revision history, hosted storage) are behind a subscription; you can avoid that cost by arranging your own sync, but it requires extra setup and possible compromises. (obsidian.md)

2) Performance and scale realities​

For users with many thousands of notes, real‑world performance problems can appear: large graph visualizations can take long to render or become unusable, search can be sluggish depending on client and platform, and certain community plugins may introduce latency. Obsidian users report that the global graph and some heavy plugins are the usual culprits as vaults grow. The combination of large attachment sets, thousands of notes, and many plugins can amplify these issues. (forum.obsidian.md, reddit.com)
The MakeUseOf author found that searches slowed and the graph view became impractical on older hardware — a common, reproducible pain point for workspaces that focus on heavy visualization of link topology. Moving to a system designed around a compact database and built‑in indexing changed that cost profile. Joplin’s offline‑first database and focused UI reduce the number of moving parts and, for many users, improve perceived speed for common tasks. (joplinapp.org)

3) Reduce maintenance overhead​

Obsidian’s power comes with maintenance: plugin updates, occasional config breakage, and file‑level housekeeping (link repair, frontmatter consistency, template drift). For people who value action (calendars, tasks, projects) over structural elegance, spending hours tuning a vault isn’t a net win. Joplin’s tighter feature surface — Web Clipper, notebooks, to‑dos aggregated into dashboards, and a single sync configuration per device — can be less taxing to operate day‑to‑day. The author’s workflow (clip → notebook → to‑do → sync) demonstrates a streamlined approach with fewer moving pieces.

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What Joplin delivers: features that matter​

Core capabilities (practical, verified)​

• Offline‑first, cross‑platform apps: Desktop (Windows, macOS, Linux), mobile (Android, iOS), and terminal clients are available so data is always accessible locally. (joplinapp.org)
• Sync options: Joplin supports multiple sync targets including Nextcloud, WebDAV, Dropbox, OneDrive, Syncthing, and Joplin Cloud. This flexibility lets users pick their trust model (self‑hosted Nextcloud, a familiar Dropbox folder, or a peer‑to‑peer approach). (github.com, joplinapp.org)
• End‑to‑end encryption (E2EE): Joplin supports E2EE to secure notes when they are sent to a remote sync target, requiring manual enabling and an initial synchronization step to propagate master keys across devices. The encryption model is well‑documented. (joplinapp.org)
• Web Clipper: Browser extensions for Chrome and Firefox allow clipped content (selection or full page) to be captured and saved cleanly into Joplin. The workflow described — clip selection, open the new note in the app, and file it into a notebook — is supported by the official clipper. (joplinapp.org)
• Project and task support: Notes can include markdown checkboxes and Joplin has explicit to‑do items which are aggregated into unified lists and dashboards across notebooks — useful for converting research into actionable steps. (joplinapp.org)
• Export and import: Joplin can export/import Evernote (.enex), JEX (Joplin export), Markdown, HTML, and PDF, enabling portability and migration. The .jex bundle includes attachments and metadata and is commonly used for backups and vault moves. (joplinapp.org, reddit.com)
• Split edit/preview: Desktop clients have a paneed experience with an editor on one side and rendered preview on the other, which reduces mode switching and accelerates formatting tasks. This is a core design pattern Joplin uses to reduce friction in writing and formatting. (joplinapp.org)

UX and workflow strengths​

• Notebooks as project containers: Joplin’s hierarchical notebooks map naturally to projects. The author’s pattern — top‑level “3D Printing” → project “Cat Guard” → sub‑notebooks for R&D and checklists — is a supported and repeatable approach that keeps project artifacts encapsulated.
• Clipping and preservation of formatting: The Web Clipper preserves images and useful links while stripping harmful or noisy site CSS when using clip selection; the authored workflow demonstrates a low‑maintenance capture cycle.
• Cross‑device sync without subscription: Because Joplin supports many backends, you can synchronize securely without paying a vendor subscription if you already have cloud storage or a Nextcloud instance. This eliminates a recurring cost and simplifies onboarding for users with existing cloud plans. (joplinapp.org, github.com)

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Tradeoffs, limitations, and security realities​

No tool is perfect. Here are the important technical tradeoffs and potential risks to weigh.

1) Database model vs. file‑per‑note portability​

Obsidian’s biggest strength is its transparent storage model: every note is a plain markdown file in a folder you control. That means you can use any editor, version the vault with git, and move files easily. Joplin manages notes in an application database (SQLite) plus attachments in a resources directory; you can export to markdown or .jex for portability, but the day‑to‑day storage isn’t the same as a simple folder full of .md files. For many this is acceptable — for others it’s a philosophical dealbreaker. (joplinapp.org, reddit.com)

• Practical bottom line: Joplin offers export to Markdown and .jex, so portability exists — but it’s not the same live filesystem model as Obsidian. If your working assumption is “I must always be able to open each note as a plain file with a text editor,” confirm Joplin’s export workflows meet your recovery and archival needs. (reddit.com)

2) Encryption nuance: remote protection vs. local at‑rest​

Joplin’s E2EE is designed to protect notes stored on remote sync targets so that servers (including third‑party clouds) can’t read your data. The official documentation makes this clear and explains the master key process. However, operational reality is that decrypted content exists on each device that has been authorized; Joplin’s local database (SQLite) will hold readable content for normal day‑to‑day operations. Community discussion confirms this nuance: E2EE protects the sync target and transmission, but local decrypted copies are available while the client is in use. That distinction matters for regulatory or high‑security contexts. (joplinapp.org, reddit.com)

• Practical mitigation: If full disk‑level encryption at rest is required, ensure the host device uses OS‑level encryption (BitLocker, FileVault, LUKS), and combine this with Joplin’s E2EE for remote protection.

3) Plugin ecosystem: smaller, but deliberately curated​

Obsidian’s plugin ecosystem is enormous and gives power users near‑infinite ways to customize behavior. Joplin supports plugins too, but the selection is smaller. That reduces complexity and the chance of plugin‑introduced breakage, but it also means certain niche workflows that were trivial in Obsidian via a community plugin may require manual workarounds or custom scripts in Joplin. (joplinapp.org)

• Practical advice: List essential plugins or features you rely on in Obsidian and verify whether Joplin or third‑party tools can replicate them before committing migration.

4) Export quirks and filename handling​

Community reports show that HTML export can create non‑intuitive attachment filenames and that some markdown exports may not be perfectly round‑trip friendly for every other app. The .jex export bundles everything, but note history is typically not preserved in some export/import scenarios. Test your critical import/export path before finalizing a migration. (reddit.com)

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Migration tactics and a practical checklist​

If the above tradeoffs sound acceptable, here’s a pragmatic migration plan drawn from the MakeUseOf workflow and community practices.

• Inventory your Obsidian vault
• Catalog plugins, workflows, attachments, and automation you rely on.
• Identify notes with heavy attachments (PDFs, large images).
• Export from Obsidian (if you want a snapshot)
• Export a complete copy of the vault (plain files). Keep a timestamped archive.
• Import into Joplin
• Use Joplin’s import (Markdown + resources) or build a phased migration by topics (projects first).
• For Evernote imports, use .enex; for Joplin, .jex is the native bundle format for backup/restore. (joplinapp.org, reddit.com)
• Configure sync
• Choose a sync target (Nextcloud or WebDAV recommended for privacy; Dropbox/OneDrive are supported too).
• If you require remote encryption, enable Joplin E2EE on a single trusted desktop client and allow it to fully synchronize before adding other devices. Follow the documented master key propagation steps to avoid key mismatches. (joplinapp.org, github.com)
• Validate exports and backups
• Export a JEX file weekly for early checkpoints.
• If portability is mission critical, test re-importing a JEX into a fresh instance to confirm fidelity.
• Recreate critical automation
• If you relied on Obsidian plugins to generate tasks or custom queries, build new workflows in Joplin using notebooks, tags, and to‑do aggregation or supplement with external task managers integrated through your usual pipeline.

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When Obsidian remains the better choice​

There are clear scenarios where Obsidian is still the stronger option:

• If you need raw file-level portability and prefer to keep your notes as editable .md files in a folder monitored by your own tools (git, text editors).
• If your workflow depends on unique, mature Obsidian community plugins or Canvas-style visual tools that have no Joplin equivalent.
• If the visual graph and a deep web-of‑links are core to your creative process and your hardware comfortably handles the rendering.

For the MakeUseOf author, however, the math tipped toward Joplin: fewer subscriptions, faster search and clipping on older devices, and a lower cognitive tax for maintenance.

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Final verdict and recommendation​

The MakeUseOf migration from Obsidian to Joplin is a vivid example of aligning tools to work style rather than prestige or popularity. The technical verification shows:

• Joplin is a fully capable, open‑source note and to‑do app with flexible sync backends and documented E2EE for remote protection. (joplinapp.org)
• Obsidian’s built‑in Sync is paid and intentionally positions convenience and advanced features behind a subscription, though users can still roll their own sync with third‑party cloud providers. (obsidian.md)
• Large vault performance is a real and user‑reported issue with Obsidian’s graph and plugin combinations; careful vault design or plugin discipline mitigates this, but it’s not a universal non‑issue. (forum.obsidian.md, reddit.com)

Recommendations for readers considering a switch:

• If your priorities are control, low cost, reliable sync, and low maintenance, test Joplin with a single project first. Use a Nextcloud or WebDAV target and enable E2EE only after validating the initial sync process. (joplinapp.org)
• If you prize raw file access, plugin capabilities, or graph‑driven ideation and are willing to manage plugins and possible subscription costs for hassle‑free sync, keep Obsidian and optimize the vault (selectively disable heavy plugins, consider splitting very large vaults). (forum.obsidian.md, obsidian.md)
• Regardless of platform, keep periodic exports and at least one full archive (JEX or a zipped vault) to avoid lock‑in and make future migrations clean. (reddit.com)

The bottom line: the tools that help you think are the ones that remain invisible while you work. For users exhausted by constant upkeep, Joplin’s pragmatic, open approach can be a refreshing and defensible alternative — and, as the MakeUseOf author shows, switching to a simpler, controlled sync model can restore focus to actual work rather than tool maintenance.

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Source: MakeUseOf I switched from Obsidian to this actually open-source app and I’m not going back