Best Reference Managers for LaTeX & BibTeX 2026: JabRef vs Zotero (Better BibTeX) vs Mendeley vs Citavi

Choosing the best reference manager for LaTeX is not the same decision as choosing one for Word. The moment you commit to a LaTeX workflow — whether locally in TeXstudio or in Overleaf — the game changes. You need a tool that produces clean .bib files, generates stable citekeys you can actually type, handles BibLaTeX field mapping without corrupting capitalisation, and ideally keeps your bibliography in sync with your .tex project without manual exports every time you add a source. Most general reference manager roundups skip these specifics entirely. This one does not.

This comparison evaluates JabRef, Zotero with the Better BibTeX plugin, Mendeley, and Citavi on the criteria that actually matter for LaTeX users in 2026: BibTeX and BibLaTeX export quality, citekey control, Overleaf integration depth, sync reliability, and cost. If you write in Word, the general Zotero vs Mendeley vs EndNote comparison covers your workflow. If you compile with pdflatex, lualatex, or xelatex, read on.

LaTeX-Specific Comparison Table

The table below focuses exclusively on criteria that matter in a LaTeX workflow. General features like PDF annotation or social feeds are excluded.

JabRef — The Native BibTeX Manager

JabRef for Beginners (Part 2) — citing references in Word and LaTeX, by James Azam PhD (London School of Hygiene and Tropical Medicine). Covers citekey setup, BibTeX export, and LaTeX integration workflows.

JabRef is the only major reference manager built around .bib files as its primary storage format rather than a proprietary database. There is no export step: your library is a .bib file. You can open it directly in a text editor, commit it to version control, and reference it from any LaTeX project without conversion.

Citekey management

JabRef generates citekeys using a fully configurable formula system. You can define patterns such as [auth:lower][year], [authEtAl:lower][year], or any combination of author names, year, title words, and journal abbreviations. Once generated, keys can be pinned so they never change — critical when you have a manuscript with hundreds of cite{} calls spread across multiple .tex files.

Overleaf synchronisation

In December 2025, JabRef announced native one-way bibliography synchronisation with Overleaf via Git. The workflow pushes your .bib file to a GitHub repository; Overleaf fetches it from there. This creates a clean pipeline — JabRef → GitHub → Overleaf — without any Dropbox dependency or manual re-upload. For teams using Overleaf’s free tier (which cannot link Zotero directly), this is a meaningful alternative.

BibLaTeX and journal abbreviations

JabRef supports both legacy BibTeX and modern BibLaTeX entry types natively. Switching between the two is a setting, not a re-export. It also ships with a comprehensive journal abbreviation database, allowing automatic expansion or contraction of journal names — a feature absent from Mendeley and requiring manual configuration in Zotero.

Limitations

JabRef’s interface is functional rather than elegant. Researchers accustomed to Zotero’s browser-clip-and-forget workflow will find JabRef more manual. There is no mobile app, and cloud sync relies on Git rather than a consumer-friendly cloud account. If your workflow extends outside LaTeX into Word or Google Docs, JabRef’s Word plugin is rudimentary compared to Zotero’s.

Zotero + Better BibTeX — The Flexible All-Rounder

Zotero is the most popular open-source reference manager among researchers, and its default BibTeX export is adequate but not great: citekeys are Zotero-internal identifiers (e.g. smithSmithetal2024 with inconsistent capitalisation), the .bib file is static, and there is no live sync. The Better BibTeX (BBT) plugin by Emiliano Heyns transforms this entirely.

What Better BibTeX adds

BBT gives Zotero four capabilities it lacks natively for LaTeX workflows:

• Custom citekey formulas. Define patterns like auth.lower + year or [authEtal2:lower:replace=.,_][year]. Keys are generated deterministically and can be pinned per-entry.
• Auto-export. BBT can watch your Zotero library or a collection and continuously export a .bib file to a local folder. The moment you add a reference in Zotero, the file on disk updates. This file can then be placed in your Overleaf project folder via Dropbox or Git sync.
• BibLaTeX export. BBT exports a proper BibLaTeX-formatted file with correct field names (journaltitle instead of journal, date instead of year), not the mangled output Zotero’s built-in exporter produces.
• LaTeX-safe field encoding. BBT handles special characters, Unicode, and title-case protection correctly, avoiding the double-brace pitfalls of Mendeley’s exporter.

Overleaf integration

Overleaf’s native Zotero integration allows premium subscribers to link a Zotero library directly to an Overleaf project. Overleaf creates a read-only .bib file and syncs it on demand. This requires a paid Overleaf subscription (Overleaf Commons, group, or individual). For users on Overleaf’s free tier, the BBT auto-export to a Dropbox or Git folder achieves the same outcome without a paid plan.

Limitations

BBT is a community plugin, not an official Zotero product. Each major Zotero update (Zotero moved to version 7 in 2024) can temporarily break BBT until Heyns releases a compatible update. During those windows, the auto-export feature stops working. Zotero 7’s new storage model has been stable with BBT since mid-2024, but this dependency risk is worth noting for teams with strict reproducibility requirements. The plugin also has a learning curve: configuring citekey formulas requires reading documentation that assumes familiarity with regex-like syntax.

Mendeley — Basic BibTeX, Significant Caveats

Mendeley, now owned by Elsevier, remains widely used in academia, partly because it is free and partly because many supervisors recommend it by default. For a general Word workflow, it is serviceable. For LaTeX, it has concrete problems that have persisted for years.

BibTeX export problems

Mendeley’s BibTeX exporter has two well-documented issues:

1. Title capitalisation. Mendeley wraps the entire title field in braces — title = {{The Influence of Priming on Recall}} — which instructs BibTeX to reproduce the capitalisation literally. This overrides any bibliography style’s case-transformation rules, producing inconsistent output across a reference list.
2. No journal abbreviations. Mendeley does not support journal name abbreviation databases, meaning you must manually maintain abbreviated journal names if your target journal requires them.

No live sync and no citekey control

Mendeley generates citekeys in a fixed AuthorYear format with no formula customisation. When you add new references, you must export the .bib file again and replace it in your LaTeX project manually. There is no auto-export or watch-folder capability. For a dissertation with 80+ sources added iteratively over months, this manual cycle becomes error-prone.

Mendeley does support linking to Overleaf, but the integration is limited to providing a .bib download rather than live sync. The University of British Columbia’s library guide summarises the situation accurately: the BibTeX file needs to be in the same folder as your LaTeX file and will not update automatically.

Citavi — Solid Export, Windows-Only

Citavi is dominant in the German-speaking academic market and is widely licensed by Swiss, Austrian, and German universities. It offers thoughtful BibTeX export features that Mendeley lacks — but its platform limitation disqualifies it for many users.

BibTeX and BibLaTeX export

Citavi provides separate export filters for BibTeX and BibLaTeX, which matters because the two formats use different field names and entry types. The Citavi BibTeX export documentation describes customisable field mapping and built-in support for specific TeX packages including natbib and jurabib. Citavi can also parse your .tex file and export only the references actually cited — a useful feature that reduces file size and eliminates unused entries from the compiled bibliography.

LaTeX support activation

LaTeX features are not enabled by default. You must activate them via Tools → Options → Citation → LaTeX support. Once enabled, Citavi integrates with TeXstudio and WinEdt for direct citation insertion, functioning similarly to Zotero’s word processor plugins but for LaTeX editors.

Overleaf and cross-platform

Citavi has no native Overleaf integration. The workflow is manual: export a .bib file, upload to Overleaf. Citavi is Windows-only; macOS and Linux users have no official path. A Citavi Web version exists but lacks the full feature set of the desktop application, and its BibTeX export capabilities are more limited.

Which Should You Use?

The right choice depends on two variables: how central LaTeX is to your workflow, and whether you use Overleaf or a local TeX installation.

On the question of managing your actual reference list count and structure, thesis citation count benchmarks by discipline can help you calibrate how large your .bib file needs to be before choosing a tool built for scale. JabRef handles libraries of thousands of entries without performance degradation; Mendeley can slow noticeably on large databases.

For broader citation style guidance once your bibliography is in shape, the Harvard referencing guide covers in-text author-date format rules that apply whether you compile in LaTeX or write in a word processor. And if you are working on citation accuracy more broadly — including AI-generated reference risks — the best AI citation checkers in 2026 are worth reviewing before submission.

For researchers working with bibliographic data and citation management alongside your writing, Tesify Auto Bibliography handles citation formatting and reference list generation directly within your thesis draft — useful when you need consistently formatted citations but want to stay focused on writing rather than managing .bib file syntax.

Frequently Asked Questions