Obsidian
Drop-in replacementFree with paid extrasThe official Linux version. Same app, same vault folder, same plugins.
Your files: Your vault is a folder of plain markdown files. Copy it across and nothing changes.
Does Obsidian run on Linux?
Verdict: Yes
Yes. Obsidian publishes Linux downloads as an AppImage, a Snap and a Debian package, with a Flatpak as well. Your notes are plain files, so the whole vault copies across untouched.
Obsidian's download page offers Linux builds in several formats, including an AppImage, a Snap, a Debian package and ARM builds for machines like the Raspberry Pi. There is also a Flatpak on Flathub, which the Obsidian team have verified, although they note they do not support it themselves.
The reason this is one of the smoothest moves you can make is that Obsidian never locked your notes up. A vault is an ordinary folder full of plain text files on your own drive. Copy that folder to the Linux machine, point Obsidian at it, and everything is there, including folder structure, links between notes and attachments.
Community plugins and themes live inside the vault folder too, so they come along with it. A small number of plugins that reach out to Windows-only software will not work, but the great majority are just code running inside Obsidian and behave the same.
If you pay for Obsidian Sync, that keeps working and will pull the vault down for you rather than you copying it by hand. If you were syncing through a cloud folder instead, set that up on Linux first and let it settle before you start editing on both machines.
Obsidian on Linux, and alternatives
Logseq
Different way of workingFreeFree alternative that also works on plain markdown files in a folder, built around daily notes rather than a page-first layout.
Your files: Reads markdown files from an Obsidian vault, though links and embedded blocks need tidying.
Joplin
Close matchFree with paid extrasFree and open source, with its own syncing to a cloud folder of your choice. Simpler than Obsidian and less to configure.
Your files: Imports markdown files and folders, but stores notes in its own database afterwards.
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