From Obsidian to Zotero

Hello everyone,
Sorry in advance if the topic is already open somewhere on the forum. I searched but I didn't find it...
I write down most of my research on Obsidian in order to dissect the concepts. I recently discovered the Obsidian Zotero integration plugin. Wonderful plugin that allows me to integrate my annotations made on zotero automatically into obsidian. I also set up this plugin so that I can link to the zotero PDF from obsidian if I want to cite it.

However, when I want to write a scientific paper or a thesis, I need to collect all my obsidian notes into one document. I do this in Word which allows me to use zotero and thus facilitate my bibliography creation.
However I need in this case to re-cite each source with the "Add citation" on word.

To optimize my workflow, I was wondering if some of you could find a way to integrate a script in obsidian (preferably with the Zotero integration plugin) (e.g. [article name](script) ) so that when I copy and paste my note from obsidian to word and refresh somewhere in word, zotero automatically detects that I am making a citation and includes the citation in the bibliography without me having to go through "Add citation".

I don't know if I am clear enough...
I have been looking for 2 days if something like this exists, without success. Thanks in advance to all the people who will take the time to answer me even to tell me if it is impossible!
  • I don't think that's possible, but maybe it is.

    Alternatively, you could avoid Word entirely and use Pandoc to create your bibliography based on Pandoc citekeys inserted into your markdown document. You are probably aware, but if not, the Obsidian Zotero Integration plugin has an autocomplete dialogue for inserting such citekeys. Just type @ to insert a citation, and a dropdown dialogue will autocomplete what you type after @. If this doesn't work, you probably need to update Better Bibtex in Zotero.

    Then, you can either use the Pandoc plugin (not maintained for a while, but still works), or the Enhancing Export to export the document with bibliography and everything as PDF or Word or whatever. The Word export will not have citations formatted as fields, as they would be if inserted in Word, so you cannot edit them after exporting.

    Pandoc plugin:
    Enhancing export:

    There is also the Longform plugin, which can help you combine notes into one document. Alternatively, the Text Transporter plugin makes it easy to transclude or copy blocks into another document.

    Text transporter:
  • edited March 11, 2023
    Hi ingmar93 and thanks for your answer !

    I didn't know this trick with the @ but it didn't work for me even if my Better Bibtex is updated. I will look for it !

    I had a look about pandoc plugin which seems to be in development and not working well for me (didn't find pandoc on my pc even when I write down the path) but seem's great especially to turn link into text ! Enhancing export plugin works for me but there is some error (if I have to export in pdf for exemple) and no possibility to transform link into text like pandoc plugin

    Longform plugin is just mindblowing ! I'm very impressed but I don't think I need this level of complexity !

    Text transporter seems good to but I don't want to increase the complexity of my system. I will stay on my copy and past method even if I've duplicate in my vault !

    Thanks for the time you spend to answer to me and for let me discover all thoses plugins !

    I will continue to use bibliography in my way hoping that it will be solve one day haha
  • @Mathunter Sorry for the late response. I hope you have figured out a workflow that works for you! I just wanted to mention that the issue with the autocompletion is being open on GitHub, so it's not just you:

    Regarding not converting the link to text in Enhancing export compared to the Pandoc plugin, @danieltomasz in the Obsidian Discord shared a solution using Lua filters for Pandoc there today:


    I wrote a proof of concept filter that do that (past discussion in the previous link) :

    Proof of concept of naive Lua filter removing wikilinks (should be the same effect as the Python script one) , if someone want to try, it should be saved to folder with markdown with Lua extension (for example 'cleanwiki.lua' and flag '--lua-filter=cleanwiki.lua' should be add to pandoc command or the same line as a pandoc_args: to yaml

    function Str (str)
    return (str.text:gsub('%[%[', '')
    :gsub('%]%]', ''))


    To use it, save it to the Pandoc directory in a subfolder called "filters" (create it if necessary).
  • Hi @ingmar93,
    I think we're going to talk every 2 months :)
    I found a good way to do what I wanted by viewing this [video](
    Thank you very much for your answer because I think I will be able to fix little problems of export mention in this video and do exactly what I was looking for at the beginning!
    I don't have the time right now to do it, but I will keep you updated when I will !
  • Update :
    I've tried to apply the method of this video ( The result is you can export a word document from a note in your obsidian vault with the citation format you want and a bibliography. But, according to the subject of this post, you CAN'T create the "magic link" in your citation that you have when you cite in word using zotero. So it means that you CAN'T re-upload your bibliography automatically in word if you do some modification after the export from obsidian to word.

    So I've look on forums and some articles and I found some new solutions !
    1) I find a way to edit everything you need in obsidian. You can put figure and auto number them, auto-number the titles, cite easily and, right at the end, export in word or in PDF. So maybe you don't need to use word at all ! That is a huge step (I don't like word). All the worklow is explained [here]( by Leonardo Castorina. (premium access on medium).
    2) Thanks to this [article]( by Alexandra Phelan (premium access on medium too) it offers different ways to do it if you struggle with the previous article. It also gives you a good philosophy to use zotero.

    So I didn't solve my first problem but the system (zotero x obsidian) I use now please me very much ! I import everything that interested me in obsidian and if I want to go back in the original file in zotero I have the link to the exact location. I write my manuscript in obsidian and wait the very end to export it in PDF. If I need very specific formatting, I export it to Word and finish the formatting here.

    I hope this could help someone else. It's thanks to dozen of post like this one that I succeed in finding my system.


  • @Mathunter that's really helpful. Thanks so much for this updated thread by all involved!
  • Glad to see it help !
  • edited November 14, 2023
    @Mathunter Thanks for all the information.

    I'm facing the same problem. I prefer Obsidian to Word, but when I have to send a paper or a fragment of the thesis to the supervisor I have to do it in Word. Also they are used to make corrections using Word revisions, so it's not easy for me to transfer those changes again to obsidian.
    Also the fact that Obsidian to word creates fixed bibliography instead of the Zotero plugin codes makes it more difficult.

    I'm searching for a way to solve this problems, but it seems to be difficult.
  • @juant Yes I agree ! Obsidian to word is much more convenient if you have some teacher or master who want to add modification to your paper.
    If you find a way I will be glad to learn from it and I'm sure other people will as well !
    We keep in touch !
  • For thosewho are still looking for a way, I FOUND IT !
    Thanks to some obsidian user (see here it seems that pandoc has a functionnality that allow to convert your citation in word zotero magic citation. Luckily it uses the same obsidian plugin that I have described before (Enhancing export plugin) so it's very easy to install if you have try my way of doing
  • > Luckily it uses the same obsidian plugin that I have described before (Enhancing export plugin) so it's very easy to install if you have try my way of doing

    Just for clarification, you don't actually need the Enhancing export for this, it works plain Pandoc as well. But yeah, it works through Enhancing export, just as any other Pandoc argument.
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