How to Use Zotero to Organize your Research

This post is part of a series on Personal Knowledge Management, or how to save your notes, files, and other important info in a simple-to-use, organized way.

Intro: Setting Up a PKM | Part 1: Google Drive | Part 2: Zotero | Part 3: Taking Notes in Notion

Zotero is how I perform feats of research magic. I use it to:

  • Store references;
  • Cite references and create formatted bibliographies;
  • Organize my research;
  • Manage my digital library;
  • File my reading notes.

It’s like having a personally curated library. The first thing I do when I start a project is search my references and call up my reading notes.

Zotero isn’t hard to use, but it has a learning curve and it can be a bit technical to get all the best functionality out of it. After years of user experience, here’s my guide to using Zotero, from configuring the app to setting it up and using it day-to-day.

Zotero has tons of functionality that I won’t cover here, including lots of nerdy advanced features (and also a few basics that are frustratingly missing, such as deleting autofill entries). You can find thorough how-to’s in Zotero’s Documentation. Below, I’m aiming to give you a start-up guide that’ll have you up and running in an organized way that’ll hopefully save you later headaches.

Table of Contents

About Zotero

Zotero is an open-source reference manager that is fully featured and free to use. (No affiliation, just a superfan.) A reference manager is a database that stores information about books, articles, and other media and outputs them in the format that you see in footnotes and other forms of academic citation. Ever tried to put your finger on that article you read once about that one topic? Forgotten how to cite a podcast in APA style? That’s what a reference manager is for. They’re generally used by academics, but are terrific for anyone engaged in research and writing.

There are a number of them out there, including EndNote (paid), Mendeley (free, with a focus on quantitative research), and RefWorks (paid). Zotero is my favorite due to its robust set of plugins that allow you to work all sorts of research miracles, like finding an article you read ten years ago, skimming your notes on it, and sending it to a colleague—in, like, 30 seconds.

In addition to storing references and outputting them, Zotero can siphon bibliographical info off the internet, making it easy to create a large, searchable database of current literature in your field(s) of interest.

Installing Zotero

Zotero is a stand-alone software program which you can download (free) for Mac, Windows, Linux, and iOS. There is also a web-based version, which you could use by itself, though it’s a lot clunkier for everyday use and I don’t recommend it. (Zotero also offers a lightweight bibliography maker tool.)

Configuring Zotero

Zotero has three default columns under the navigation menu:

  • On the left, the organization panel;
  • In the center, a list of your references;
  • On the right, the bibliographical info for the selected reference.

You can drag the bars around to resize each column. You can also customize your display and change which columns are shown under the View Menu.

To begin with, you’ll have an empty database. You can import references if you have them stored elsewhere (File Menu > Import). To input your first reference manually, click on the little green “plus” button over the reference list or go to File Menu > New Item > (select item type). You can also paste from your clipboard: File Menu > Import from Clipboard. To import automatically from the internet, see below under Using the Zotero browser extension.

Setting up your reference list

To sort your ref list, click on the field you want to sort by (Title, Date, etc.). A little arrow will appear after the field name indicating that that’s the sort field and whether it’s ascending or descending. Click again to change the order from ascending to descending or vice versa.

To customize the fields shown in the reference list, right-click on the top bar with the field names in it.

Syncing your Zotero data

Zotero gives you the option to sync your reference data to their cloud so that all your bibliographical data is automatically backed up. Highly recommended. Go to Edit Menu > Preferences > Sync Tab. You’ll need to register for a free Zotero web account (or log into your existing account if you have one), then link your account.

The free plan easily covers just the reference data, meaning that the bibliographical info and notes that you enter into Zotero can be automatically backed up. (I have thousands of entries in my database and I’m fine on the free plan.)

There is a low data ceiling for free syncing, which means you can’t store your article PDFs, eBooks, or other large files on Zotero’s servers without a paid plan. That’s not a bad option; they’re a nice nonprofit worth supporting. However, if you already pay for cloud storage somewhere, you can easily link your files on whatever cloud drive you use (I use Google Drive) to Zotero. I’ll show you how to accomplish this below under PDF article storage.

Setting up your output format

If you need to submit a paper with citations formatted in a particular style, such as Chicago, MLA, AMA, Nature, APA, or any of a hundred other technical formats, you can select the styles you need to have as options under File Menu > Preferences > Citation Tab. You’ll then be able to select which one of your active styles you want for output.

To output a reference, right-click on it and select Create Bibliography from Item… Alternatively, you can create bibliography as you go within Word or Google Docs; for how to do this, see below under Using Zotero integrations.

You can also specify a default style for copy-and-pasting from Zotero under File Menu > Preferences > Export Tab. Mine, for example, is set to Chicago 17th (full note) and I use it all the time. Just hit Ctrl-Shift-C to copy and when you paste the ref will be in your specified style. You can also drag-and-drop into many programs.

After Zotero’s latest update to version 6, which was a major update, a lot of the functionality that used to be done with plugins is native to the app. Many of the new features, particularly the excellent built-in PDF reader, are accessible to all. However, other features are really only relevant to those who store their PDFs in the Zotero cloud, which effectively means purchasing storage. Again, this is not a bad deal, especially if you have a relatively small library, but if you don’t want to invest, then you’ll want to read on about plugins.

To give you an idea of scale: I have a large library of just under 18,000 references/6,500 PDFs, which clock in at ~15GB, meaning I would need the unlimited plan which is currently $120. I already pay less than this for 2Tb elsewhere, so I’d rather link my files. Also, heads up, since there is no Zotero Android app, some functionality is limited to iOS on mobile. This might be relevant to you if you like to read and annotate articles on a non-Apple tablet, although note that in order to read on an iPad through the native reader you have to use the Zotero cloud. You can use any tablet to read and extract annotations if you install the ZotFile plugin and use a PDF reader like Adobe’s.

A full list of Zotero plugins with descriptions is available here. I’m going to highlight my favorites below, but ymmv. Mostly, I highly recommend ZotFile; it’s the only plugin you’ll need to accomplish the things I talk about in this guide.

To install a plugin to Zotero, first download the program file from the plugin page, then go to Tools Menu > Add-ons > Click setting gear > navigate to downloaded file > Click “restart.”


The ZotFile plugin allows you to do five crucial things by adding menu options when you right-click on a reference:

  • Attach the last downloaded file in a specified folders (such as your computer’s “Downloads” folder) to a given reference (for how-to, see below under PDF article storage);
  • Rename your downloaded files with one click according to a naming convention that you determine (how-to also under PDF article storage);
  • Move your files with one click into whatever location you want to store them in (how-to also under PDF article storage);
  • Send files to your tablet or other device (including your desktop), effectively creating a reading list for yourself that conveniently opens in whatever reader you like to use, like Adobe Acrobat (for how-to, see below under Taking notes with Zotero);
  • Extract highlights and other annotations you make on a PDF and put them into a Zotero note for you, so you can quickly skim through your own notes int he future (how-to also under Taking notes with Zotero).

You can configure Zotfile in Zotero under Tools Menu > ZotFile Preferences.


Zotilo is an advanced plugin that not everyone will need, but it can be handy in certain cases. If you ever find yourself moving your PDF storage location, needing to apply a new naming convention to your files, or do other kinds of tedious batch-editing tasks, Zotilo is your friend. Download from Github and configure under Tools Menu > Zotilo Preferences.

Other Plugins

  • If you’re a Notion user, Notero is great for connecting selected refs between your Zotero and a Notion database.
  • If you’re a WordPress user, Zotpress lets you easily use Zotero refs on your website.

Manually backing up your Zotero Data

Although you should enable cloud sync, it’s a good idea to have a local backup copy of your Zotero data so you can restore it, move between computers, etc. To make a manual copy, locate your Zotero data, close Zotero, and copy your data directory (the entire folder, including zotero.sqlite and storage and the other subfolders) to a backup location. (I do this on the first of the month to my external HD.)

Organizing your Zotero


Zotero’s top-level category is a called a Library. Your default library is called My Library. You can have multiple libraries, but each one is a separate database. For example, you could set up one called My Home Library for books you own and keep at home. Or you could separate your science articles from your history articles. You can also have collaborative group libraries; more on that below under Collaboration in Zotero. I use the default My Library for all my refs.

Collections and Subcollections

You can organize your top-level Library into Collections and nested Subcollections. These hold specific references from your Library. There’s lots of different ways to use Collections: you could make a Collection for a given subject you’re researching, for courses you teach, use one as a reading list, or, as I mainly do, to organize a bibliography for a writing project.

To make a new Library or Collection, click on the icon on the far left below the Menu (circled in orange in the image above) or right-click on a Collection to manage it and create Subcollections.

My recommendation is to avoid organization schemes that require a lot of manual sorting because they aren’t useful without a lot of maintenance. I mostly use one collection called “Writing”; I then make subcollections for each writing project I’m working on. This makes it easy to see what I’ve already cited, remember works I want to use or need to read, and to make the bibliography. I also have a “Reference” collection.


You can also tag your refs, manually or automatically.

To tag automatically, go to Edit Menu > Preferences > General Tab and select the “Automatically tag” entry under Miscellaneous.

Adding a tag to a reference manually

To tag manually, click on the Tags tab in the right column and then tap the “Add” button. (Yep, you can use emojis.)

You can search your tags in the search box below the tags display at the bottom of the left column.

To select the options you want for tags, click on the small colored squares below the tabs display on the bottom of the left column. (Above left.)

To manage your tags, including to assign colors to them like I’ve done, right-click on a tag. (Above right.) You can use up to nine colors.

I personally don’t use subject tags; instead, I use tags to visually distinguish references, such as multiple editions (so I don’t delete them as duplicates) or primary sources. Another usage is to create lists for myself, like books I need to look up next time I’m at the library or articles I want to read.

Relating refs to one another

You can also set up relationships between references using the “Related” function. You can use this to do things like connect individual chapters in a book, reviews to the reviewed item, or different editions of a book.

Using Zotero integrations

Zotero offers two important types of what they call connectors, which connect between Zotero and your web browser, and Zotero and your word processing app. The first allows you to save references from the internet. The second one allows you to search and insert citations from within your doc.

The Zotero browser extension

Zotero offers browser extensions for Chome, Firefox, Safari, and MS Edge. Once the extension is installed, it’ll automatically activate when you’re on a webpage that has relevant metadata. The icon will change to show you what kind of reference Zotero has identified: book, article, book chapter, podcast, etc. Click on the extension and the bibliographical data will be downloaded to Zotero for you. Zotero has to be running first; you’ll be prompted to open it if it’s not. You can choose to save it into a particular Collection: a pop-up window will load once you click the extension. I like to give the data a quick once-over after downloading and change anything manually if needed.

If there is an open-access PDF on the site, it’ll be automatically downloaded as well. However, telling Zotero how to name and store it are tweaks you’ll have to do (only once though)⁠—more on that below.

Zotero integration for Word, Google Docs, or LibreOffice

First, find and install the integration you need. This will add a Zotero menu to your word processor. The first time you click “Add/edit citation” in a new document, you will need to initialize the document by selecting your Zotero account in the pop-up (you can do this through Google authorization, making it a one-click operation). Next, you need to minimize your word processor/browser window (crucial step) and follow the prompts from Zotero that come up behind it. This process (which is only a few clicks) has to be repeated in new browser windows/documents; it’s not a one-time thing.

PDF article storage

Another core use of Zotero is to manage your PDF library. I’ll say right off the bat that it isn’t an all-in-one digital library manager, because such a unicorn sadly doesn’t (yet?) exist. For example, you can’t store Kindle books directly in Zotero because Amazon won’t let you, let alone collect all your eBooks from different services all in one place (sniff). But for any article or book PDFs you’ve got, Zotero is an amazing solution for storing the file with all its bibliographical info in a searchable interface.

If you’re planning to store your PDFs in Zotero’s cloud, all you need to do is make sure you have File Syncing checked. Go to Edit Menu > Preferences > Sync Tab > tick the box for “Sync attachment files in My Library using Zotero. (I believe this is selected by default.)

If you want to store your files on your own hard drive or cloud drive, read on. You can read Zotero’s explanation of the difference here.

Specify your PDF folder location

First, decide where you’ll be saving your files. Then, go to Edit Menu > Preferences > Advanced Tab > Files and Folders Tab. Copy the file path into the Base directory or browse to it using the “Choose” button. This will tell Zotero to look for your PDFs in that specific folder. Meaning, when you click on an ref with a linked PDF, it’ll magically open in your reader of choice.

Choosing a naming convention

Using Zotero alone, you can simply right-click on a ref and select “Rename File from Parent Metadata.” Of course, if the file doesn’t have good metadata, this won’t help you out, and that’s where Zotfile comes in. To tell Zotfile how to rename your files, go to Tools Menu > Zotfile Preferences > Renaming Rules Tab. You’ll see different options spelled out for you as well as a box for displaying your chosen format. Then, you can right-click > Manage Attachements > Rename.

If you’d like to rename your file and whisk it away to your chosen storage folder all at the same time, go to Tools Menu > Zotfile Preferences > Settings Tab. There you can specify your storage folder. Then, right-click > Manage Attachements > Rename and Move.

Using “Attach New File”

In the Tools Menu > Zotfile Preferences > Settings Tab, select your “watched” folder. Mine is simply my computer’s Downloads folder. You’ll then be able to right-click > Attach New File for any reference and the last downloaded file in your Downloads (or other) folder will magically get attached, renamed, and moved.

Taking notes with Zotero

Zotero Notes

One of the great features of Zotero is the ability to take notes on a given work and attach them to it. You can make “child notes” associated with a reference or “standalone notes” that act like a reference in themselves. Notes now have rich text and markdown features. The first line will preview under the reference in the main Library window.

A few ways I use notes are:

  • To directly type notes;
  • Copy-and-paste a table of contents;
  • Note a book’s library catalog number if I use it often;
  • Copy-and-paste highlights from services like Kindle or Scribd;
  • Extract highlights and annotations made in Adobe Reader or in Zotero’s PDF reader.

Using the Zotero PDF Reader

Zotero’s built-in PDF reader is feature-packed. It uses a tabbed interface that allows you to open multiple articles and display related notes, data, contents, and other options in the sidebars. I’ve switched to using it consistently for research reading.

Downloading annotations from PDFs

To download highlights and notes made in the built-in PDF reader so that they appear in an attached Zotero note (and not just in the reading pane), go to the ref in your library, Right-Click > Add Note from Annotations.

Using Zotero with Adobe Reader

You’ll need to use Zotfile in order to read your PDFs remotely in Adobe Reader (or another PDF reader of your choice) and then extract the annotations. You don’t actually have to read them on a tablet; you could use this just as well to read and extract annotations all on your main computer.

To do this, first create a folder to hold the articles you’re currently reading and annotating. Mine is inside the Google Drive folder that holds all my PDFs and is named Zotfile. You’ll send files you want to read and highlight to this special folder by Right-Click > Manage Attachments > Send to Tablet.

Then, open up your file to read it from within this folder (on your tablet, phone, computer, work computer, wherever). Highlight to your heart’s content. When you’re done, on your main computer, Right-Click > Manage Attachments > Get from Tablet to retrieve your file and place it back in its home in your library folder. If you’ve made annotations, you can extract them at this point too.

Downloading annotations from PDFs

To download highlights and notes made in Adobe or elsewhere, go to the reference, then Right-Click > Manage Attachments > Extract Annotations. You can set up your preferences for how this is done in Tools Menu > Zotfile Preferences > Tablet Settings Tab. For example, you can tell Zotfile to save your highlighted file separately from the clean copy.

Collaborating in Zotero

You can create Group Libraries to share with others or collaborate on creating a resource list. Groups can be public/open membership, public/closed membership, or private. You need to create your group and send invites (if closed membership or private) via Zotero’s web interface here.

Tamar Ron Marvin Avatar

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13 responses to “How to Use Zotero to Organize your Research”

  1. Atara Cohen Avatar

    This is awesome!

  2. Liz Shayne Avatar

    This is awesome! I started using Zotero with my dissertation and now use it to keep track of basically every topic I find interesting.


  • 💬 Tamar Ron Marvin

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