Using Syncthing for syncing markdown files (Obsidian)


I’m wondering if anyone has any suggestions for my specific use case. I have a work computer and a personal computer with a separate Obsidian vaults (they are essentially just folders with markdown files) on each. Ideally I’d like to merge the majority of the contents of the vaults into my personal computer, but not all of the contents.

More specifically, in my work vault, I have notes on random research papers etc… that I would like to merge with my personal vault, and I also some data that could be considered sensitive and I would prefer not to merge with my personal stuff (just in case) - all of this data I don’t want to merge is located in a single folder within the vault. I would like to have this merge between the work research papers and personal vault to be bi-directional, i.e. if I edit that note on my personal laptop, the changes also show up on my work laptop, and vice versa.

However, I only want the notes that originated from the work laptop to be bi-directionally synced, i.e. I don’t want my work laptop to have any visibility of my personal notes.

Is this something that is feasible to set up? Or should I just live with having 2 vaults (i.e. separate folders)

Thank you!!

Someone more familiar with Obsidian will have to provide a definite answer, but if Obsidian folders on the disk use their normal names (which seems to be the case), it may be possible to just utilise ignore patterns to sync only the folders that you need (see However, please experiment with temporary files first before trying this out on your real note files.

I don’t use Obsidian much, but the PIM I use shares a similar disk storage format.

If the merge involves making the “work” vault a subdirectory under the “personal” vault, that would be straight forward with Syncthing’s file ignore patterns feature.

But if the work vault is supposed to overlay the personal vault – i.e., they each have similar subdirectory trees and relative file pathnames – then it could get messy very quickly.

Internal links…

If the work vault is a subdirectory of the personal vault, there’s no guarantee that internal links between notes/pages will work because the root of the vault is no longer the same for the work vault while it’s on your personal computer.

Vault settings…

Obsidian uses a hidden directory named .obsidian at the root of a vault to store preferences and other stuff.

As a subdirectory of the personal vault, the work vault’s .obsidian directory can be included in the file sync, but it won’t be used by Obsidian without some creative workarounds. The work vault just looks like a branch of the personal vault, so it’ll be using the personal vault’s settings.


I think the cleaner and safer option is to first manually merge your work vault with your personal vault – preferably as a subfolder of your personal vault.

Once you’re satisfied with the new vault, use Syncthing to sync it between your personal and work computers with a simple ignore pattern (on the personal computer side) to filter out everything except the path to your Obsidian settings (optional) and your work subfolder like so:


/Work is relative to the root of the Syncthing folder and not directly associated with the location on your personal computer – i.e., C:\Users\Sov\Obsidian. So Syncthing would be looking for C:\Users\Sov\Obsidian\Work.

As long as you put stuff you want accessible at work under /Work, no personal notes and/or files will “leak” onto your work computer.

Be sure to carefully read the Syncthing documentation page linked to by @tomasz86 before syncing between your personal and work computers. Ideally, try it out between two personal computers first to iron out any issues.

(I haven’t personally tried the above with Obsidian, but it’s the approach I’ve been using with Zim.)

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