Zotero for researchers — a beginner's guide

What is Zotero?

Zotero is a free, open-source program that helps you collect, organize, read, and cite research papers. Instead of keeping hundreds of PDF files in random folders, Zotero stores everything in one library.

With Zotero you can:

• Save papers from PubMed and journal websites with one click.
• Organize papers into collections.
• Read and annotate PDFs.
• Add notes that stay attached to the paper.
• Insert citations while writing.
• Create a bibliography in thousands of journal styles.

If you write scientific papers, Zotero is one of the most useful tools you can learn. It is run by a nonprofit, your library lives on your own computer, and it works offline.

Install Zotero

1. Go to zotero.org/download.
2. Download Zotero for Windows, macOS, or Linux.
3. Install and open the program.
4. Create a free Zotero account if you want syncing and the iOS/Android apps — Edit → Settings → Sync, then sign in.

Your library is now ready.

Install the Zotero Connector

The Connector is a browser extension. It lets you save papers from websites with one click.

1. Go to zotero.org/download/connectors.
2. Install it for Chrome, Edge, Firefox, or Safari.

When you find a paper on PubMed or a journal website, click the Zotero button in your browser toolbar. The reference — and the PDF, when one is freely available on that page — is saved directly into your library.

Cite in Word, LibreOffice & Google Docs

Zotero includes plugins for Microsoft Word and LibreOffice. They are installed automatically with Zotero and appear as a Zotero tab or menu in your word processor.

If the tab is missing: Edit → Settings → Cite, then click the install button for your word processor and restart it.

Google Docs works too — the Connector adds a Zotero menu to Google Docs automatically, with the same workflow.

Organize your library

Create collections for your projects. Example:

• Lung Cancer
• Asthma
• Systematic Review
• Methods
• Statistics

A paper can belong to several collections without being copied — collections are labels, not folders.

Use tags to mark the state of papers. Examples: Read, Included, Excluded, High quality, Needs review.

Read and annotate PDFs

Zotero includes a built-in PDF reader — you do not need another program. You can:

• Highlight text and underline important findings.
• Add comments in the margin.
• Jump between annotations.
• Search inside PDFs — across your whole library.

Your annotations stay linked to the paper, and you can pull them into a note with one click (Add Note from Annotations).

Make notes

Each paper can carry notes. Good notes are short and factual:

Later, you can search these notes across your whole library — which is when they start paying you back.

Insert citations

1. Open your document and place the cursor where the citation should appear.
2. Click Add/Edit Citation in the Zotero tab.
3. Type an author name or a few words of the title.
4. Select the paper and press Enter.

Zotero inserts the citation automatically:

Smoking increases COPD risk (Smith et al., 2024).

Change citation style

Different journals use different citation styles. You never edit citations manually: open Document Preferences in the Zotero tab and choose the style — Vancouver, APA, Nature, BMJ, JAMA, and thousands more. Every citation in the document updates automatically.

Create a bibliography

When your paper is finished, click Add/Edit Bibliography. Zotero creates the reference list from the citations in the document. If you change the citation style later — or add and remove citations — the bibliography updates too.

Attach open-access PDFs with FullVahti

FullVahti is a free, open-source Zotero plugin from Vahtian. It finds legal open-access full-text PDFs for papers already in your library — via Unpaywall and PubMed Central — and attaches them to the right records, with an honest report of what it could not find. It never bypasses a paywall, and nothing is sent to external AI services.

Install FullVahti

1. Download the latest .xpi file from the FullVahti releases page.
2. In Zotero: Tools → Plugins.
3. Click the gear icon → Install Plugin From File… and select the .xpi.
4. Restart Zotero.

Run it

Choose the collection you want to process and run FullVahti on it. It checks every paper and labels the result:

• PDF found — attached to the record.
• Already attached — skipped.
• No legal open-access copy found — reported honestly, not hidden.
• Manual review needed — for you to decide.

Many researchers only need this much: save references to Zotero, run FullVahti, read the attached PDFs inside Zotero. No other Vahtian tools are required.

Better BibTeX for LaTeX & R workflows

Better BibTeX is a free community plugin that gives you more control over citation keys and exports. It is especially useful if you write in LaTeX, Quarto, R Markdown, Obsidian, or any Markdown/Pandoc workflow.

Install Better BibTeX

1. Download the latest .xpi from the Better BibTeX releases page.
2. In Zotero: Tools → Plugins → gear icon → Install Plugin From File…
3. Select the .xpi and restart Zotero.

Why use it?

It creates stable citation keys — readable keys like smith2024copd that stay the same even if you edit the reference later, so your LaTeX and Markdown citations never silently break.

Automatic .bib export

1. Right-click a collection → Export Collection…
2. Choose the Better BibTeX format.
3. Tick Keep updated.

Every time you add or edit a reference, the .bib file updates automatically — ideal for LaTeX, Quarto, and R Markdown, where the bibliography should rebuild reproducibly.

A simple research workflow

1. Find papers.
2. Save them to Zotero with the Connector.
3. Run FullVahti to attach available open-access PDFs.
4. Read and annotate the papers in Zotero.
5. Write your manuscript with Zotero citations.
6. Before submission, use CiteVahti to examine whether each cited source actually supports the sentence it is attached to — it checks claim–source support, not truth, and you make the final call on every claim.

FullVahti finds the documents. CiteVahti helps you examine what those documents actually support. They solve different parts of the same workflow — and Zotero holds it all together.

Common questions