Zotero integration, while maintaining existing folders in zotero

Things I have tried

I’ve watched a lot of youtube tutorials, have read the documentation on the zotero integration plug-ins I’ve found, and searched through the forum.

What I’m trying to do

I’m new to Obsidian (but not new to markdown), and would like to integrate zotero with it. I’ve watched several tutorials and looked at the options for different zotero integration plugins, and I like the idea of each paper in my zotero becoming its own obsidian note, with the notes and highlights i’ve taken in zotero migrating into the obsidian note. The issue I’m having is that my zotero has over 1500 papers and they are really well organized into folders and subfolders in my zotero itself, but none of the integration methods I’m seeing allow for that in obsidian–they just dump every paper into the same folder in obsidian, which would just be unmanageable for me. Is there any way to maintain the same folder system I have in zotero in the integration with obsidian? Alternatively, I’d be fine with each folder becoming its own note, and the info for the papers within that folder being added to the note itself, say under different headers.

I know that obsidian is more for links etc and have had friends recommend I not rely on folders as much, but I know myself and know that I will not use this software if I can’t organize everything into folders, because otherwise it would be overwhelming.

Thank you in advance for any advice!

You might want to ask in the Obsidian Discord’s #academia channel. (If you do that and get an answer, it’d be nice to copy it back here.)

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Where would this Obsidian (sic) #academic channel be found? A link would be helpful.



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For me, the link is a rabbit hole to nowhere???


Do you have a Discord account, and have you joined Obsidian’s Discord server?

The folder and sub-folder organization that you have created in Zotero is non-existent on your physical hard drive. You can create as many virtual locations within Zotero that you want. If you dig, you will find that your citation files still sit in their constant location (a specific sub-folder with a long alpha-text string as its name).

From my quick read, I believe your mistake is to believe that you must use Zotero and Obsidian to contain exactly the same content and to mirror each other exactly in the “virtual” organization of that content. Obsidian is better used as a tool to explore the relationships in notes that you extract from documents stored in Zotero regardless of where those documents are stored in Zotero. Obsidian is poorly used as a tool to also organize (or to re-organize) the documents that you already have stored in Zotero.

Perhaps you can train yourself out of the current habit by making a studied practice to avoid including the documents from Zotero with the export. Instead, work to assure that the notes that you export from Zotero into Obsidian have properly-formatted links to point back to the source documents in Zotero.

You are at liberty also to move notes around in your own self-created folder structure within Obsidian regardless of where those notes initially arrive.


I joined Discord at the link that was provided. Pardon my ignorance, but where is the doorway next to join the Obsidian Discord server (so as to find its #academic channel)?


You can reach it via Community - Obsidian

Hi @CawlinTeffid , why do you refer to Discord when Reddit refers to the forum as official channel?
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The Discord is official, too (see the link in the post before yours). Sometimes if you don’t get an answer in one place you can get it in the other. And Discord has that #academia channel where people talk about Zotero a lot. (And I suggested the copy the answer back here if they get one because the forum is better than Discord for longer-term reference.)

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