A different paradigm: Obsidian as an interface for the file explorer

Hey all, so I wanted to share a workflow I have adopted relatively quickly after a few iterations of my obsidian based pkm system, and though it might inspire some to follow me down the rabbit hole.

I started using obsidian like everyone through creating a vault in my documents. As notes started growing, and with them the desire to start linking to more of my university content, I moved the .obsidian one directory up and started opening my vault a level higher, to encapsulate my courses folders into the linking scope. This worked wonders. I could link to every lecture slides, pdf, or video I was given during my studies.

As a small side note, I should say that I got in the habbit very early on to download everything I could during my studies for future reference. I however realised that I just had no effective mean of accessing this information properly, and it as a result simply was left mostly dormant. Allowing for linking through obsidian simply unclocked all this knowledge.

As I further embraced the obsidian ways, I found myself wanting to also use it to manage other things, such as my administrative stuff, or finances. The issue was, this was in a other folder yet again (my folder organisation being structured around a few big folders, such as knowledge, adminstrative etc…). As a result, I moved my .obsidian folder yet again another directory up, at which point I basically found myself at the top of my entire folder structure (moving further up means starting to include computer program files in the vault).

And this is when it clicked. Obsidian doesn’t only work as a note taking app, it can also be what I didn’t realize the file explorer needed all this time: a file explorer user interface. An interface that not only lets you refer to different documents, but lets you anotate, link, and put into context as needed.

With this newfound knowledge in mind I started what to this day is the longest standing organisation scheme standing to date. I find that I nowadays almost never add something to my files without refering to it in some ways in my pkm system, and finally feel like I have truly unlocked access to my information.

As such if this post’s content is new to you, and you find yourself intrigued by this approach, I am happy to provide any extra needed information and tips or tricks I found over the last few months of living with this system (Vault structure, CSS snipets to hide folders from the vault file explorer etc…)

Cheers all!


thanks, great workflow.

I might start creeping up the file directory myself.

Apart from using Obsidian’s search syntax, operators e.g, file, path, content,line etc. I am also querying my vault/directory using advanced regex desktop search engines. If I were on Windows I would use …

Agent Ransack | screenshots

AstroGrep | screenshots

grepWin | screenshots

DocFetcher | screenshots


On my chromebook with Obsidian for Android I use grep

aGrep Android app





I can then easily open them in Markor which looks at the same vault folder/file directory as Obsidian.

[PS: for compatibility, in Files & Links …

I’ve disabled [[Wikilinks]], yet I still get the advantages of [[]]

Default location for new attachments
In subfolder under current folder
Subfolder name

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I’d be using Obsidian at the top of my system too, if I weren’t using Obsidian Sync. Unfortunately Sync’s vault-size limit is too small for that — and if it weren’t, my phone and tablet’s storage are too small to store a vault that size. I’d worry about performance, too, if Obsidian had to index all of my many files. But ideally I would have Obsidian or something like it atop my whole system.

To do something similar I’ll use Markdown links for items outside the vault. I should find an app or script to automatically check for broken links, since Obsidian doesn’t update those when the target is renamed.


I’ve been doing something along similar lines. I throw documents of all different formats into my Obsidian vault, mainly markdown and Microsoft Word. I use both folders and linking extensively, and flip between the system file explorer (Finder on the Mac) and navigating with obsidian. I wish obsidian‘s native file explorer was more robust, but I live with what it is.

I ran into the same issue, and solved it as follow. My folder structure is as follows:

  • Documents:
    • 0-Obsidian_Vault
    • Knowledge
    • Administrative
    • etc…

I then open my vault at the “Document” level, but only sync at the “0-Obsidian_Vault” (which only contains my notes linking to everything else). This way you can link to anything, but all you notes are still nicely contained within a single vault that can easily be exported/backed up/synced without having to take the rest of the file explorer content with it.


I used to do this too, but found that keeping a vault separated from the rest meant I had an easier time syncing or backing up my notes alone. That being said I completely agree with you, a more robust built-in file explorer would go a long way to improving this workflow!

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Thanks for the great sharing! I too use obsidian to act as a portal to some of my daily document folders. Lately I would like to implement this to my office and make a document index system which would share with my colleague, but found that there’re two challenges for me:

  1. since our folders are stationed on an NAS shared drive, and not all the folders I would like to be included in this “index”, so a hyperlink to the selected folders or documents would be a better way. But there seems no easy way to update or manage shared folder paths as hyperlinks in obsidian

  2. we use both windows PC and Mac, and they treat folder path of a shared drive very differently. So it seems to me that I have to type 2 different hyperlinks to a single document in order to accommodate both OS system. Which is a real pain

Due to my limited IT knowledge, I’m not sure if there’re better ways to achieve this, maybe I could get some enlightenment from all of you here. :slight_smile:

You might have better luck posting those questions as their own help threads so more people will see them.

I have tried to use obsidian for file management too. There is a need for making notes for files and I think it is really powerful, but I gave up because of syncing and back up was a problem. And I was not sure about performance issues. I think I may give it another try after reading this, I am specially interested if you have a way to add notes to non-md files. Like scripts for it or something, that can be inspiring for others like me.

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I wonder if you still want to share these tricks with us, i am contemplating using such a scheme but need to know more on how and where to start.

Hey @Archie, appologies for the late reply (I have been away from the forum for a while). Adding notes to non-md files was basically one of the initial driving factor for the method described above. There is however no real means of doing that as far as I know. My approach as such has been more to create a “meta-note” if necessary, which could be named the same as the matching file and stored with it. There are also a few extensions assisting in that. The new pdf plugin lets you do just that for example.

However I should say that I find it more convenient to work the other way around. That is, not annotating on a file basis, but topic/subject basis. This allows for having a single meta-data note refering to multiple files.

Hope this helps!

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Hi @Iv3llios!

I’ve found your post so intriguing because it hits all the right spots for me. I’ve always wanted to integrate my files (kept in a google drive folder) with my notes. None of the other tools allowed me to do that because they all had their own “internal filesystems” (e.g. OneNote, Notion, Bear, TheBrain, etc.)

I just wanted to ask, are you still using Obsidian as an interface for the file explorer? If you do, have you made any more tweaks to it? Have you seen any drawbacks? Finally, I do not understand how are you syncing your files? I saw that you are using a separate folder inside your file structure to keep your notes, but are you using Obsidian Sync or some other third party solution to sync your notes? How could I sync just my notes while using Google Drive?

Thank you so much in advance!


Glad to help! Yep very much still using it, not much has changed though and it remains as effective as originally described. Regarding the sync of files, all I do is have virtually everything on onedrive (in my system, what I call document in one of my previous replies is actually the onedrive folder). This way whatever I do get synced across my machines and phone (I use onesync for the phone, I believe there is a Google drive equivalent). Only main drawback is the admittedly slower starting time for obsidian. But its just a matter of waiting a few seconds so not too problematic.

Thanks again for chiming in!

I’ve adopted your system, the only difference being that I use Google Drive instead of OneDrive. Like you, the only drawbacks I’ve experienced is somewhat slower startup time for Obsidian, and the inability to use Obsidian on my iPad (but that’s due to Apple’s walled garden more than anything).

Since you’re so much further along than me, could you perhaps just outline a few of the benefits you’ve seen with this system?

Hi, I want to achieve this for my research project. Could you share a picture of your vault structure please? I hame some practical questions. How do you manage pictures embeded in your notes (general folder, local folder or next to each note)? How are you using tags? Do you use Zotero/Mendeley citation?

The vault structure is pretty arbitrary. The only thing that matters is having the following in place:

  • Obsidian-vault folder (l1)
    • Note vault (l2)
    • Regular documents A (l2)
    • Regular documents B (l2)
    • Regular documents C (l2)

I then decided to keep all content related to my note in the Note vault. There it is divided as:

  • Misc
  • Files and Figures
  • Knowledge
  • Projects
    • Project 1
    • Project 2

MOC goes into misc, figures (and very occasional files) go into files and figures, and the rest goes into Knowledge if it is knowledge (no sub-folders), or project if it is project-related information (each project gets its folder). Everything put together looks roughly like that:

  • Obsidian-vault folder (l1)
    • Note vault (l2)
      • Misc
      • Files and Figures
      • Knowledge
      • Projects
        • Project 1
        • Project 2
    • Regular documents A (l2)
    • Regular documents B (l2)
    • Regular documents C (l2)

The key perk of this approach is that if you open your vault at l1, you can link to everything. Yet since all your notes themselves are in a separate folder, it is easy to just back those up (using git for example) without including all the other files you are linking to (so if you have a lot of lecture videos for example like I do this is very convenient).

I haven’t found a good solution for zotero yet aside from using the zotero plugin currently in beta (it lets you insert citations and links to open a paper in zotero, which is good enough I guess).

Hope that helps!

Im doing some of this. I actually use Eagle (eagle.cool) for most of my file management, better to see and preview files +tags and notes attached to each, and despite being media focused it can import all filetypes - but that comes with a caveat, in that eagle import/copy files inside its own folder structure, so i still have outside folders, and im still deciding how much to use ‘inside’ obsidian itself.

That coupled with multiple hard-drives (my main files separated amongst then) and i wouldnt be able to just pour it all into Obsidian… but ive found workarounds

Junction Folders: its a feature of the ntfs fileformat, and in short its like a ‘shortcut’ folder that for all intents and purposes makes the OS think its actually there. Deleting a junction folder just deletes its junction(the shortcut), but any changes inside work as intended… and the most interesting part: the OS sees the filepath as a normal folder.
So 2 folders, C:/1 and D:/2, could stay where they are and both be under a vault somewhere else (say F:/Vaul/2)
I know theyre possible on linux and mac (heck probably even android) both i only learned on windows- where i use Link Shell Extension, and its a simple right click away from windows explorer then a ‘paste’ at destination (its imediate, nothing is copied)
PS: just keep in mind copying a vault will copy its junction folders as if they were normal, so junctions wouldnt solve syncing/cloud storage issues

External Links/Embeds: I dont want to put too much strain on Obsidian puting a huge folder under it just to reference few of its files (Obsidian performance decreases with too many files)- in my case i have A LOT of reference and stock images (and with chaotic filenames) to ever make sense via Obsidian.
I just link external- [](full file path) and it work wonders, can even embed (pictures only, idk why obsidian allow embeding some external fileformats and others not, like pdfs)
I know theres a few applications(at least on windows) for copying a files fullpath quickly, in Eagle its a quick right click choice so its working wonders for me

Hardlinks: Just like junctions its a function of ntfs- files CAN be in multiple places, actually being there, in a better way then shortcuts and with safety (deleting one of its incarnations wont delete the others). They could even have different filenames and still be the same (any changes made in one will affect all others, even if renamed).
And they can also be done quickly with Link Shell Extension mentioned above- hundreds at once if needed…Its another way to have just some files or part of a folder inside Obsidian, that will sync the actual files (unlike shortcuts) - and its a way to have files in different folders saving space (the data on the disk is the same, a single location in the disk platters)
Theres only 2 things to consider:

  1. Hardlinks only work on the same hard drive
  2. Theyre trickier to delete (fully) and can make folder size comparisons weird

It works like this: a file in multiple places(hardlinked) is only truly deleted completely if all instances of it are deleted. They take no extra space but theyre just entries for the actual data- only deleting all instances actually deletes them. That is a plus for safety, but can also lead to deleting files for clearing space yelding no space gain.
The OS recognizes then and will show a disk full storage just fine no matter how many hard links it contains- but comparing folder sizes will become misleading with too many hard links… because ive hardlinked a huge folder inside eagle and parts of it inside obsidian, the folder size of each combined is greater then the hard disk theyre in. Overlap.

Partial Vault Nesting: Im not using sync(yet) but i already have a plan: a folder inside a vault being another vault, the main one that is synced; On desktop using the top level vault with more files. It can be easy to avoid any issues by having all actual notes (.md) inside the main vault only (the synced one).

On desktop any and all links and embeds will work fine- but im guessing on mobile a bunch of them will become ‘broken’… but would it matter so much? The data/note will be there, it will become a case of some notes not showing their reference file on the go- and just some files… and as needed back on the desktop just a case of moving some select files that one wants to access on mobile to the synced vault- all links to it will update… with a good clear folder structure for that it would be easy to even swap files in-out, keeping the main vault(synced) always lean

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Thanks for the post and how are you using it today (Obsidian+Eagle.cool)?
I’m trying Eagle, I tried a graphic where there are about 200k files and strangely it works pretty well, same with 10k videos in another library.
So I’m trying to link with Obsidian, so far it’s not working well. It won’t open the direct link to the file, probably because of the structure/complexity of the link, and the link to open in Eagle, it only opens the active “library”.
Then there is the option of using the API that Eagle provides.
So I find this post and nothing else near it, which is a pity because maybe Obsidian+external images/videos would be an interesting solution.