Connecting Zotero and Evernote

For collecting and managing references and scientific publications I use Zotero because it has a nice browser integration. You can simply click on the Zotero icon and the reference will be automatically saved to Zotero including the full-text PDF (e.g. on IEEE Xplore), title, author, entry type (e.g. journal article, website, thesis, book), etc. You can arrange your findings using folders for different topics and even use an entry simultaneously in multiple folders without having duplicate files. After collecting references I export them in BibTeX format to use them in TeXlipse.

Although Zotero can store various file types such as text, audio, video, images and much more I prefer Evernote for organizing my notes, writing paper summaries and collecting ideas. Now we need a way to connect both worlds. ;)

The Goal

Ideally, I would select a reference in Zotero, press CMD+C to copy its absolute URI, select some text in Evernote, add a hyperlink to the URI and that's it. The result would be a link in Evernote which brings up the reference in Zotero when I click on it. Well, let's see what is possible.

Some apps support a certain URI scheme to give other applications access to their content. E.g. in Evernote you can copy the link of a note and get something like evernote:///view/12345689/s123/.../ which can be used to create clickable hyperlinks between your notes. Zotero is also capable of creating and understanding links but it takes a custom translator-plugin to access it. First you have to distinguish between the Zotero item URI, which is in fact a web URL pointing to the reference in your Zotero online account (, and the Zotero select link that is the desired URI in the format zotero://select/items/0_XXYYZZAA. Based on the translator-plugin by nschneid I created my own simplified version that exports only the plain URIs of the selected elements by using the shortcut CMD+Shift+C.

Now that we have the URI for accessing the reference it's time to make use of it. Evernote is a very smart program but sometimes it's too smart. When you create a link it only supports URLs that start with the common schemas such as http, https, ftp, ssh, etc. Using a zotero://... URI the "OK" button is simply deactivated and adding the link is not possible. To create clickable Zotero select links it is necessary to enable intelligent links (right click > replacements). This way pasted Zotero select links are automatically converted in clickable links when you hit enter! :eek3:

(It is possible that the URI is not associated with Zotero and nothing happens when you click on it. What helped in my case is to create a .html file containing a hypertext reference such as <a href="zotero://select/items/0_XXYYZZAA">My Link</a>, open it in your browser, click on it and make sure to allow your browser to open Zotero for this specific URI schema.)

Summary / TL;DR:

  1. Goal: Create clickable links in Evernote pointing to Zotero entries
  2. Zotero: Install my customized translator-plugin (download on GitHub Gist)
  3. Zotero: Select entries, press CMD+Shift+C to copy the item URI
  4. Evernote: Right click > Enable Intelligent Links
  5. Evernote: Paste item URI and press enter
Links to Zotero entries in Evernote

Links to Zotero entries in Evernote

The connection of Evernote and Zotero is awesome for managing references, writing summaries, collecting ideas and organizing research. :}

9 thoughts on “Connecting Zotero and Evernote

  1. Pingback: RTF-Links from Zotero in Evernote | brain.flush();

  2. Eli

    Thank you, this is exactly what I was searching for. Unfortunately, I did not understand how to activate this option in Zotero... what do I do with the .js file? Moreover, I did not find anywhere right click--> replacements in Evernote. There is a 'right click-->substitutions--> smart links' option, but it does not let me insert zotero links. Any suggestions?


    1. Flo Post author

      Hey Eli,

      thanks for you comment! You have to put the .js in the translator folder of your Zotero library folder. Here is a guide on how to locate it:

      AFAIK the intelligent links can also be activated in the preferences or are activated by default... Usually it just works if you type a URL in an Evernote note and hit enter. The URL should be converted to a clickable link automatically. Maybe you should just try this :)

      Kind Regards

      1. Eli

        Hi Florian,

        Thanks for the answer. I got your js to work (one has to change the export format in Zotero Preferences to ZotSelect Link after adding the js file to the translators folder).

        However, there is no option in Evernote for enabling 'intelligent links', such that one gets stuck with a link that one cannot click on in Evernote. Evernote isn't smart enough to recognize Zotero://... as a link. I'm using Evernote 6.0.2 for Mac. I wonder if there's still a solution for that problem... it would be great to get this to work!


        1. Flo Post author

          Hi Elisha,

          you are welcome!

          What happens if you write an URL in an Evernote note and press enter afterwards? Does it turn blue and clickable? If yes, then intelligent links are enabled. Now this should also be working for zotero://-links if you press enter after pasting them.

          If that's not working for you, you may want to take a closer look at my follow-up post:

          In this post I'll explain how to take this whole Zotero-Evernote connection a step further. The final workflow is like this:
          - Select entries in Zotero
          - press CMD+Shift+C to copy the HTML links
          - Press CMD+CTRL+Shift+C to convert the HTML code in the clipboard to RTF
          - Paste links in Evernote

          Maybe you'll give this solution a try. :)

          Kind Regards

  3. Roberto

    hi Florian,
    I have downloaded and Installed your translator plugin.
    It generate the right URI, and in Evernote the Hyperlink is active, however when I click on the Hyperlink a W8 windows pops up telling that there is no app availible to manage that link thus W8 does not pass on to zotero the link.

    any suggestion to overcome the problem ?


    My configuration is as follows:

    Firefox 34.0
    Zotero (plugin)
    Windows 8

  4. Pingback: Zotero links | pashtetgp

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