Becoming a Zoteroist

For years, I used Zotero primarily to generate BibTeX files for citations. But the hard disk crash on my laptop (2 Jan 2025) was a wake-up call. It made me realize the importance of a robust, cross-platform management system to organize and safeguard all my resources, including library structure, books, notes, links, annotations, and progress.

After exploring different options, I realized I already had the perfect tool: Zotero! Since then, I’ve been delving into it, and now I happily call myself a “Zoteroist”. In this post, I’ll summarize the core features of my setup, which will also serve as a handy reference for reproducing it on a new machine. Let’s dive in!

File Syncing

Zotero’s syncing process consists of two parts:

• Data syncing: This handles the syncing of library items, notes, links, tags, and other metadata — everything except attached files.
• File syncing: This manages the syncing of attached files, such as PDFs, audio and video files, images, and more.

Zotero’s free plan provides limited cloud storage, which is sufficient for data syncing. However, storing my entire library of resources (primarily PDFs) requires significantly more space. So, I had always considered it unsuitable for my needs. But this time, after re-evaluating and digging deeper, I discovered an excellent workaround that I had previously overlooked: WebDAV. And I’ve since integrated Zotero with the WebDAV server of Koofr, which provides ample storage to meet my requirements.

Click to view my settings

Edit > Settings > Sync:

I’ve also set it up on my iPad’s Zotero app for seamless syncing across devices.

Plugins

To enhance Zotero’s interface and functionality, I’ve installed the following plugins. Below, I might only highlight the settings I’ve customized, the rest remain at their defaults.

• Better BibTeX
  Click to view my settings

  Edit > Settings > Better BibTeX:
  [Update] My current Citation key formula is:

    auth.lower + year + '_' + shorttitle(1).lower
  

  [Update] For Add URLs to BibTeX export, I am choosing in the 'note' field.

  Edit > Settings > Export:
  Quick Copy’s Item Format is set to Better BibTeX.

• Notero
  Click to view my settings

  Edit > Settings > Notero:
  

  Alongside Notero’s Github page and my template¹, these tutorials² can be helpful to set up Notero.

• ZotMoov
  Click to view my settings

  Edit > Settings > ZotMoov:
  Even though I sync files with WebDAV, I have still kept this ZotMoov setup to send PDFs to Dropbox to edit (i.e. adding bookmarks) with iPad’s ‘PDF Expert’ app. I have connected Dropbox account with my PDF Expert app.

  The steps to follow:

  • Double-click on an item or its attachment and select ZotMoov: Move selected to Directory in desktop Zotero.
  • Get and edit the PDF in 'PDF Expert' app.
  • Double-click on the item and select ZotMoov: Move selected from Directory back in desktop Zotero.

• PDF Background
  Click to view my settings

  Edit > Settings > Zotero PDF Background:
  On a side note, the option Use Dark Mode for Content needs to be disabled to keep these background colors unaffected from the system dark mode.
  

• Reading List
  Click to view my settings

  Edit > Settings > Reading List:
  

• arXiv Workflow
  Click to view my settings

  Edit > Settings > arXiv Workflow:
  

• Zoplicate
  Click to view my settings

  Edit > Settings > Zoplicate:
  

• Add-on Market
• Chartero
• Open PDF
• ZotMeta
• Ethereal Reference
• Better Notes
• Folder Import
• Get Date from URL last-modified
• Del Item With Attachment
• Others that I kept disabled for now:
  • Ethereal Style
  • Actions and Tags
  • Google Scholar Citation Count
  • Zotero Citation Counts Manager
  • Bionic for Zotero Reader
  • ZoTTS

Extras

• File Handling and Renaming
  Click to view my settings

  Edit > Settings > General:
  Customize Filename Format... I prefer this Filename Template:

    {{ firstCreator suffix=" - " }}{{ title truncate="100" }}{{ year prefix=" (" suffix=")" }}  
  

• Advanced
  Click to view my settings

  Edit > Settings > Advanced:
  

• Rofi Louncher Integration (May 1, 2025)

  I have started using a lightweight Rofi launcher script to quickly search and open PDF attachments from my Zotero library.

  Features:

  • Shows item type, author, year, and title
  • Connects with the native Zotero database
  • Launches PDFs with the preferred viewer
  • Fully keyboard-navigable
  • Customizable theming

  So far, I’ve just tweaked the script to include item types and configured its theme to fit my setup and taste. I’ve also mapped it to Super+Z for instant access!

  Here’s a preview:

Present Issues

Zotero’s PDF viewer still lacks:

1. highlighter/marker pen
2. eye-friendly or custom background color

I’ve grown more inclined to use Zotero’s PDF viewer (Zot-PDF) for convenience. However, I’m hesitant due to a couple of limitations. Alongside books and papers, I often annotate handwritten documents, where I prefer using a highlighter or marker pen. Unfortunately, Zot-PDF lacks such a highlighter pen tool. For now, my workaround is capturing areas with colored rectangular boxes or annotating with the drawing pen. I hope Zot-PDF introduces a proper highlighter tool in the future. Additionally, Zot-PDF’s appearance and background colors on iPad still need improvement. Currently, I rely on enabling Night Shift and adjusting Color Temperature globally via iPad settings. I’m optimistic these features will be enhanced by the Zotero team soon.

My workarounds are:

1. using colored rectangular box or drawing pen
2. changing appearance for eye-comfort with:
   • PDF Background plugin on desktop Zotero
   • Night Shift and Color Temperature on iPad

Final Thoughts

Zotero has turned out to be a game-changer for organizing my resources. With WebDAV for syncing and all these cool plugins, it’s become so much more than just a citation manager. If you haven’t dived into Zotero’s full potential yet, give it a shot — you might just become a Zoteroist too!

See Also

• Catherine Brendow. “10 Advanced Ways to Become a More Proficient Zoteroist.” Geneva Graduate Institute Library Blog, November 20, 2024.
• Jason Puckett. “GSU Library Research Guides: Zotero.” Georgia State University Library, September 3, 2024.
• InfoTrack. “The Advantages of Reference Management Software: The Art of Managing Your References.” University of Geneva Library, March 1, 2018.
  

Footnote

1. My Notero template is here. ↩︎

2. Tutorials on Notero:

   • Anna Everett. “A Technical Guide to Setting up Notero (Zotero + Notion Plugin).” Medium (blog), August 26, 2024.
   • The Diary of A Scientist. Ultimate Notion + Zotero Academic Database Setup. YouTube, Feb 5, 2024.
   • Holly Jane. Sync Zotero → Notion // Research Paper Workflow. YouTube, March 21, 2023.

   ↩︎