Nested vaults - usage and risks

I use nested vaults to represent concentric circles of access control, so far with good success. Eg with the following four nested vaults:

  • notes/ - private home-machine-only content, never synced via cloud, plus…
    • notes/cloud/ - private synced content, synced via encrypted cloud, plus…
      • notes/cloud/public/ - public content, mirrored to website, plus
        • notes/cloud/public/blog/ - published content, announced in rss feed.

and a bit of website scripting: when on your home machine, you can see everything. When on your phone, you see the smaller cloud-synced subset. Anyone with a web browser can see the smaller public subset. Anyone subscribed to your blog feed sees the new content in the smaller blog subset.


Periodically you can review new/edited pages to see if they should be moved to a different (more or less private) vault. In such cases you simply move the file, and your vaults mostly just keep working - a great feature of Obsidian. (Moving a page up to a more secure vault will break links to it in the less secure vault - not a problem. Often splitting the page into two is a good fix.)

Another level suggests itself: notes/cloud/groups in which each of your collaborators has a vault where they only have edit permission, and in which they can read the vaults of others group members and link to their notes. The author or anyone else reading the note can then follow the backlink.

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Hi @Ellanxis, I didn’t see your post before.

I’ll try to clarify what I meant. It was actually just a heads-up from back when people were extremely vocal about the atomicity of notes and even naming the note as the content of its thought.

So, if you’re writing a set of notes in the nested vault and make links and one points to a note named “name”, the link will be [[name]], which is also in the nested vault.

But then you open the main vault, which also has another set of notes on its level with a link [[name]]. If you surf your nested vault from the main vault, when you click the link from the nested vault, you’ll be directed to the “name” note of the main vault, not the nested one, as it should be.

Note (no pun intended) that the nested vault is never aware of the [[NestedVault/Note2]] relation. The same if you try to link something from the main vault to the nested vault and then try to open it from the nested vault. It tries to create a new note.

This is a very specific problem that is present in very, very few scenarios if any. It is very simple to solve, if you ensure you have unique names for every note across all vaults and between them too.

I hope I was able to clarify it.

any updates or changes to best practices here?

i’m currently doing my “nesting” in DEVONthink— i have like six vaults for Obsidian and then i index them all in DEVONthink in a designated DEVONthink database. this means i can work with my notes really fast regardless of how pokey Obsidian is being. i toss tons of markdown/pdf/bookmarks/articles into my DEVONthink inbox and then slide them into Vault folders as appropriate.

if i do cross-vault linking inside Obsidian it works, but i do easily end up with duplicate files and i might write something my research vault but then when i am processing my notes after a workshop i’ve facilitated. part of that are binary files that are artifacts like architecture diagrams, screenshots, that sort of thing. nesting and alias/linking would be great but i am reluctant to even attempt nested vaults.

the DEVONthing abstraction layer (well it’s a lot smarter than just random middleware i am really loving the plugins for pulling related docs from DT into my Obsidian notes, that sort of thing.

but i’m starting to get frustrated with the materials being duplicated and being difficult to track revisions to some notes or documentation or research material. it’s not the size of the data that concerns me (if it gets really top-heavy i have some options in mind) as much as the clutter and being unable to know if this is the right copy of a print-as-PDF Confluence page, or Excel and Word docs.

the idea of the sub-vault of sensitive data that needs to be available on the go. i use DEVONthink to Go (it’s been a rocky road but we’re in a good place right now) as my information retrieval and triage front-end for collected and captured things.

Well I’ve been using nested vaults now for over two years. They have become progressively more extensive and the hierachy has extended further up and down. I don’t have any vaults outside my nested system (apart from occasional test vaults) and I have experienced no problems whatever. The warnings in the early days came as a response to developer concerns with often strident warnings from moderators. My feeling is that most people would have no issues; that recovery from any issues that people somehow stumbled into ought to be straightforward. The risks are certainly much lower in terms of data loss than most of the sync solutions people use.

But the issues remain the same. Thoughtlessly accepting offers to create a new file from a link without being aware of where you are brings the possibility of filename clashes in some higher level vaults. This will never happen if all files are given unique names.

My vaults now routinely have their own folders for attachments and linked files. I make extensive use of the nested folder system outside Obsidian. Every one of my projects has a vault, some even have sub-vaults nested within them. Fleas ad infinitum.

I’m not sure I even partially understand your system, and I don’t use DT. But it seems that the problem arises thorough the interaction between your info in DT and your info in Obsidian. I don’t understand it well enough to give advice.

But I would suggest routinely adding date/time to your file names - that should at least let you identify the most recent. (I routinely use a text expander.)
It ought to be simple to use a file comparison program to identify and delete duplicates (you would need to check each deletion manually, since I suspect that you create possibilities for the most recent file not to be the most complete).


oh i’m a compulsive annotator and any output is named zettel-style. i even made a textExpander macro to do a current date-time-stamp dts and i wrote a Finder action to rename a file so i click that thing whenever i want an atomic incarnation of a file that is easily usable and retrievable by using that chronological order.

thank you for your reply! i tried to do a submodule of a repository and they don’t propogate when using Obsidian Sync. ordinarily that wouldn’t bother me and i’d use Resilio to p2p sync between devices.

but every time i’ve got a sync problem the first thing everyone on discord says is to stop using anything that isn’t a local saved vault on a computer using Obsidian Sync. i’m still testing, the real source of truth is DEVONthink.

I don’t completely understand your issues.

But, on your main device, you can select a subfolder of your main vault and open that as a new vault. The contents of that vault would be synchronised by Sync with the main vault. You should be able to open it on any device.

I don’t use Sync, so I’m not sure of which settings you would want to use. You could sync both vaults but I suspect that would open up the possibility of Sync clashing with itself.

I’m sure there is a simple solution, even using Sync, but can’t advise very well. It would be important to get the structuring of you nested system correct, if you want to sync some vaults but not others.

Are nested vaults fully compatible with Obsidian sync? i.e. no conflicts when syncing multiple vaults which are nested together.

So if my vault set up is like this:
- nested-vault/

and both vaults are being synced with Obsidian sync, are there any scenarios which might cause undesired behaviour?
an edge case I can think of is

  • editing files in nested-vault whilst in master-vault, and then editing those files again on a different device and vice versa

No, this is not supported. In fact if both vaults are open and syncing at the same time you might see race conditions between the two vaults, leading to duplications and deletions, etc.

I’ve never had a sync clash, despite working on both top and nested vaults at the same time. But I don’t use Obsidian Sync and don’t simultaneously work on more than one device.

I can see the possibility that Obsidian Sync’s vault based system could set up competing processes. In which case, I’d suggest syncing only nested vaults or only the top vault.

Anybody tried this on a jailbroken mobile device? I’d like to access a subfolder as vault which is not possible through Obsidian URI.
I tried creating a dummy vault with the required name, then created a symlink for the folder I want to access and replaced the dummy with the symlinked folder (same name).
When I was greeted with “Do you trust…?” I thought I did it but not even one md file was sitting in the vault. It did load the plugins though and the theme (which came in an .obsidian folder I synced over from desktop; I have 24 folders I want to access as nested vaults).

Any pointers, ideas?

I wrote up the nitty gritty of a workaround here:

Would this work fine if only the master-vault were set up with Sync, and the master-vault is nothing more than a container for sub-vaults, each in their own folder, with no notes of its own? That way, when working in the sub-vault, syncing would happen only when the master vault was also open, and the master-vault Sync process should keep things sorted out.

Would this work OK? I want to use this as a way to Sync more than the five-vault limit. (Of course, care would need to be taken to make sure to preserve uniqueness of note and file names across the whole master-vault.)

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This should work fine, so long as no other sync program is in use.
But you would need to watch the size limit for a vault.

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Awesome, thank you!

I just want to mention another usage of nested vault as I haven’t seen it talked off yet. Nested vaults come in handy when you want to separate notes for security reasons. For example, I can have notes containing public information in one vault. Then I can have another vault with proprietary information, which will never leave local system, but I may want to refer to my public notes. In this case, I can nest the public vault inside the private one.

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The other approach, the one I use, is to have a master vault which is not synced, and sync only sub-vaults. These sub-vaults represent my current areas of activity and I only have one level of sub-vaults in my master vault.

My master vault lives on OneDrive but is locally synced to my PC. OneDrive can restore deleted files for 30 days, which works for me.

OneDrive itself does sync. Any problems with that?