Joplin vs Obsidian: Which Free Markdown Note App Fits You?

Amira does penetration tests for small clinics and law firms. Her findings, client network diagrams and remediation checklists cannot sit on a vendor's server in readable form. She already runs Nextcloud on a box in her office and works from a Linux laptop and an Android phone.

Recommendation: Joplin, synced to her Nextcloud with end-to-end encryption turned on. Sync to Nextcloud is built in, so there is no extra bill and no plugin to trust. She should enable encryption on the laptop before the first sync, store the master password in her password manager (Joplin cannot recover it), then add the phone. Obsidian could do this with Syncthing, but she would be assembling the privacy story herself instead of switching it on.

Daniel is in year three of a PhD on 19th-century port cities. He has around 600 notes: one per source, one per concept, one per archive visit. His chapters come from noticing that a customs ledger, a newspaper and a letter all mention the same merchant.

Recommendation: Obsidian. He writes a note per merchant and links to it with [[Ezra Halloway]] from every source that mentions him; the backlinks panel then lists every source in one place, which is the chapter outline. Joplin can link notes, but its links point at internal note IDs and backlinks need a plugin. Daniel should keep the vault in a folder his university backup covers and resist installing a plugin until he has needed it three times.

Carol kept recipes, travel plans and 30 years of lesson ideas in Evernote. She no longer wants to pay for a notes subscription and wants a free app that still has notebooks on the left and notes in the middle. She uses a Windows laptop and an iPad.

Recommendation: Joplin. It imports her ENEX exports directly, keeps them in notebooks, and the three-pane layout is close to what she knows. Links between notes are "mostly preserved," per Joplin's own import docs, which matters little for recipes. Sync through the OneDrive account that came with her laptop costs nothing. Obsidian's Importer also reads ENEX, but she would land in a folder of files with a blank sidebar and a plugin browser, which is the opposite of what she asked for.

Tomás keeps design notes, on-call runbooks and a daily log for a payments team. He wants them in a Git repository so he can search them from the terminal, review changes like code, and open them in his editor during an incident.

Recommendation: Obsidian. The vault is a folder of Markdown files, so it can live in a repository, and git log becomes the note history. Daily notes and wikilinks cover the log and the runbook cross-references. Joplin keeps notes in its own database; he could export Markdown on a schedule, but the files would be a copy rather than the source of truth. One caution: runbooks with secrets in them do not belong in a repository at all, in either app.

Priya has 1,800 notes in Joplin from five years of freelance design work. Over the last year she started linking client notes to project notes and wants a backlinks panel and a graph without depending on a plugin.

Recommendation: move to Obsidian, but test one notebook first. Export a single notebook as Markdown with front matter, open the folder as a vault, and check three things: attachments, tags, and links. Joplin's links point at note IDs, so they will not resolve in Obsidian and need converting to note titles, which takes a script or a community converter. If those three survive on one notebook, export the rest. If they do not, Joplin plus a backlinks plugin is the cheaper answer.