This little tutorial on Zotero and Zotero Add-ons, will show how I have set up Zotero to store files in a separate folder, the procedure to create entries from one or many PDF’s articles, retrieving information on the PDFs, and finally renaming original files. I wrote this guide mostly for myself (to remember the configuration when I will change computer) and for friends who would like to use Zotero the way I have it set up. I suppose you already have a basic familiarity with Zotero, otherwise I recommend visiting their website to learn more.

What to Install

Here are links to relative website.

How I have organized my files

Zotero, by default, uploads your pdfs to its own cloud. When you open a pdf file from within Zotero, the file that is opened is the one that Zotero automatically created in its own internal library. I prefer to keep all my files on my hard drive, and not on the Zotero cloud.

All my articles and books are inside a folder (e.g, Books and Articles). My articles are then organized in folders by topic (e.g., Behavioral Science) and in certain cases I use sub-folders specific to a journal. The organization of folders and sub-folders is then reflected exactly in my Zotero library.

Although my Zotero organization mirrors my folders stucture, I do have extra Zotero collections created ad hoc and including entries that are a duplicate of an entry originally in another collection. For example, you might have article “A” in the collection (and folder) “Collection 1”. If you start to write an essay, you might create a new collection “Temporary Collection Essay” where you copy the article “A”. Article “A”, is now present in both Zotero collections, but the PDF file will be present only in the original “Collection 1” hard disk folder.

If this is your case than you might find this guide helpful.

How to configure plugins


If you want to keep your PDFs files in a separate folder, then you have to specify the main folder (e.g., Books&Articles). Ideally you will also have subfolders. In my case, the collection structure of Zotero is mirrored into the actual folder structure. If this is the setup you would like, then set  “Use subfolder defined by” to /%c (as on the screenshot).

ZotFile General Settings for file location and folder structure.

Another very useful setting in Zot file is “Renaming Rules”. Here you can specify the structure of the PDFs filenames when renaming the uploaded/linked files. For example, I like to have file name structure where I keep the first 3 authors last names, the date of publication, and the title. (e.g., Donkers_van Diepen_Franses – 2017 – Do charities get more when they ask more often – Evidence from a unique field experiment.pdf).  To obtain this renaming, rule I have configured ZotFile as you can see on the screenshot below.

ZotFile settings for renaming files.

Zotero Scholar Citations

No much to configure for this plugin. The only thing you really need to do is adding the column “Extra”

If you right click on an article, you can update the citation count based on Google scholar.

How to batch add PDF files, create Zotero entries, and rename the original files.

  1. Select the destination collection in Zotero (exactly the same as in your hard drive folder structure)
  2. Click on the green arrow
  3. and click “Link to File”. Select all the PDFs you want to add to a collection. The process can be very slow if you have a lot files. Prepare to do work on something else or anyway do not turn off your computer.

    As you can see on the screenshot, files are added to Zotero as attachments in the corresponding collection.
  4. You can now select all the newly added attachments, and load the metadata. After selecting, right click on the selection and “Retrieve metadata”.
    If you are doing this for a lot of files(more than 50) and using the citation count add-on, it is a good idea to disable the add-on before retrieving metadata. Otherwise Google Scholar will block your process and Zotero will start to provide a lot of annoying error messages.
  5. An extra optional step is renaming the actual PDF file based on the metadata you have retrieved. This is where ZotFile can be very useful as it provides customization of the filename structure. Assuming  you have already configured the ZotFile add-on properly, you can select all the new Zotero entries you have retrieved metadata for. Right click on the selection, Manage Attachemnts -> Rename AttachmentsAs an example the file previously named “Better-the-devil-you-know–How-product-familiarity-aff_2016_Journal-of-Econo.pdf”
    becomes “Giacalone_Jaeger – 2016 – Better the devil you know – How product familiarity affects usage versatility of foods and beverages.pdf”. Remember to configure the Zotfile add-on setting before doing this or the files will be moved to some other folder.