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Zotero Citation Software

A Guide to Getting Started and Using Zotero

Setting Up Zotero

Zotero has a large number of settings and plugins to use so you can customize Zotero to work how you want. The following information is not required to use Zotero but is offered as it is often some of the most asked questions the HJF Library gets about Zotero.

Note that all of the setting changes are made primarily in the same place in the Zotero desktop software. Open the Zotero desktop software and click the "Edit" menu at the top of the screen. From that menu, select Preferences.

This will bring up a popup menu with six additional menus: General, Sync, Search, Export, Cite, and Advanced. These are the menus we will be exploring throughout the rest of this page.

Syncing Zotero

The first thing most people want to know is how to sync or how not to sync their Zotero library to the web. This section will cover those options plus some alternative syncing options. To make things easier, we have a list of options we are going to refer to throughout this section.

  • Option 1: Do Not Sync Zotero Library
  • Option 2: Sync My Library Citations and Notes but Not Attachments
  • Option 3: Sync My Library Citations, Notes and Attachments (Sync everything)

Option 1: Do Not Sync Zotero Library

If you do not want to sync anything to the cloud and Zotero's Web Library, then there's nothing further you need to do in regards to this section on syncing. Everything will be stored on your local computer and only on your local computer. Make sure to practice safe data practices and backup your data to some alternative hard drive in case of a hardware or software failure or else you will lose all your Zotero information.

Option 2: Sync My Library Citations and Notes but Not Attachments

Option 2 is the one we see the most of. This requires an account with Zotero as it will allow you to sync your citation data to Zotero's servers and access it from the Web Library on any computer with an Internet connection, but it does NOT require that you pay Zotero for online storage. Zotero provides a small amount of free storage that will be quickly used up if you do sync attachments and not just citations and notes.

  1. Open the Preferences menu as described above.
  2. Click on the Sync Menu.
  3. Select to link your account by logging into Zotero using your Zotero login information.
  4. Once logged in and linked, new options will be available. Under "File Syncing" uncheck both options.
  5. Click "OK" button at bottom of popup screen to save your changes.

Option 3: Sync My Library Citations and Attachments

Option 3 as explained here is assuming that you have a Zotero account already and that you have decided to pay for the Zotero Storage Subscription. Go to the Sync menu under Preferences. Make sure you are logged in and your desktop is linked to your Web Library/Zotero Account. Then check "Sync Automatically" so your libraries will be syncing changes made back and forth automatically. Then check "Sync Full-text content". What this does is any PDFs that have full-text searching available will have that full-text indexed in Zotero allowing you to not search just your citations but also inside your PDFs. By syncing this, you are making sure you can also search within your PDFs from the Web Library as well.

Now, under the File Syncing section of the menu, check "Sync attachment files in My Library using" and select Zotero from the dropdown menu. We will not be discussing in this guide how to use WebDAV but if you are interested, Zotero covers that in their Forums. This ensures that your files will sync up to your Web Library.

Alternative Syncing Solutions

There are two alternative solutions for syncing. 

  • Alternative 1: Sync Attachment Links Using Web Storage
  • Alternative 2: Sync Attachment Links to Local Storage

Both of these options require that from your desktop Zotero, you right click on the source you want to attach a link to and select "Add Attachment" as shown in the screenshot below.

Alternative 1: Sync Attachment Links Using Web Storage

This option requires you have a web storage solution already in place such as Google Drive or Dropbox.

  1. Upload your attachment to your web storage solution.
  2. Get the sharable link to that document after it has been uploaded. Each service has its own way to share links. Consult their help if you need assistance.
  3. Go to Zotero desktop and click on the citation you want to add the link to.
  4. Right click on the citation and select "Add Attachment."
  5. Select "Add Link to URI" and paste the link there.
  6. Click "Save" and you are done.

When you open up the Zotero Web Library or access it from another computer and click to see that attachment, it will open your browser and require you to login unless you have the file open on the web. You can login to your web storage account and access your file directly.

Alternative 2: Sync Attachment Links to Local Storage

Alternative 2 does NOT actually sync your attachment files but links directly to them on your computer. If you are not using the computer where your files are stored, the links will not work. This is simply an option to attach files to your citations so they are more easily accessible.

  1. Right click on the citation in Zotero you wish to add a file link attachment.
  2. Select "Add Attachment"
  3. Select "Attach Link to File"
  4. Navigate the provided directory to where you stored the file you wish to attach and select it.
  5. Click "Save"


Many of us use cloud storage solutions that sync files back and forth to our computer allowing us to put files on them and having them automatically sync to our cloud storage accounts. This is NOT recommended due to numerous tests that show Zotero's database becoming corrupted and breaking using this method. Zotero's Forums are filled with this occurring even though it tends to work for a while at first. If your Zotero database becomes corrupted, there is no way to save it except from loading a backup. Make sure to have a good backup strategy in place.

Choosing the Citation Style

One of the many strengths of Zotero is the number of citation styles it provides. Because it provides so many, it is important to go in and select what style you'll primarily be using. If you do not see your style listed in Zotero, don't worry. They have an easy option for adding all kinds of different styles.

  1. Go to the Preferences Menu and select "Cite".
  2. A long list of styles will be presented. Scroll through and find the style you wish to use.
  3. After clicking on your desired citation style, click "Ok" at the bottom of the popup screen to save your changes.

Now Zotero will make sure to try and save the metadata from articles and websites when you use the browser extension to fit that citation style. It will also automatically configure your citations in a word processor when you create them to that style format. More on this can be found on the "Using Zotero", "Using Zotero with MS Word" and "Using Zotero with Google Docs" pages of this guide.