Mendeley
Elsevier's reference manager — a widely-used alternative to Zotero with built-in PDF annotation, institutional cloud sync, and a large social discovery network, though its move to a cloud-first architecture and Elsevier ownership have driven some researchers toward open-source alternatives.
What it does
Mendeley is a reference management application owned by Elsevier that combines a PDF library, citation manager, and academic social network. It lets researchers:
- Import papers via browser extension, DOI, or PDF upload
- Organize references into folders and groups
- Annotate and highlight PDFs within the app
- Generate formatted citations and bibliographies in Word, LibreOffice, or LaTeX
- Discover papers through the Mendeley Suggest feature and the social feed
Mendeley has been around since 2008 (acquired by Elsevier in 2013) and has a very large installed base, particularly in Europe and among researchers in medicine and the social sciences.
Mendeley vs. Zotero: the practical comparison
Zotero is open-source and community-maintained; Mendeley is proprietary and owned by Elsevier. For researchers who care about data sovereignty and long-term independence from a commercial publisher, this is the primary reason to prefer Zotero. Mendeley’s terms of service give Elsevier access to usage data and metadata from your library.
Mendeley’s PDF reader is somewhat more polished out of the box, with smooth annotation, highlight synchronization across devices, and a built-in note layer. Zotero’s PDF reader (added natively in version 6) is competitive but historically Mendeley had an edge here.
Cloud storage: Mendeley’s free tier includes 2GB; Zotero’s free tier includes 300MB (additional storage is $20/year for 2GB). For large PDF libraries, both require either paid cloud storage or local file management.
Institutional integration: Mendeley is deeply integrated with Elsevier’s ecosystem — ScienceDirect, Scopus, and Mendeley Datasets share the same account. For researchers at institutions with Elsevier subscriptions, this can be convenient. For researchers who primarily work outside Elsevier’s catalog, this advantage disappears.
Citation style coverage: Both Mendeley and Zotero use the Citation Style Language (CSL) and have similar breadth. Zotero’s community-maintained CSL repository is slightly larger.
Mendeley Copilot
Elsevier has added AI features under the “Mendeley Copilot” branding, including paper summarization and Q&A over your library. As of late 2025, these features are in various stages of rollout. The AI features are powered by Elsevier’s own models and are subject to change.
Limitations
The 2022 desktop app migration broke some workflows. Elsevier retired the legacy Mendeley Desktop in 2022 and replaced it with Mendeley Reference Manager, which lost several features (folder nesting, some import options, local-only mode) that power users relied on. Community sentiment around this transition remains negative.
Elsevier ownership and data concerns. Your library metadata (what papers you read, how you annotate them) is stored on Elsevier’s servers and subject to their terms of service. Researchers at institutions with complex IP policies, or who work on unpublished sensitive research, should read those terms carefully.
Less extensible than Zotero. Zotero has a rich plugin ecosystem (BetterBibTeX, ZotFile, Zotero Connector improvements, etc.) that Mendeley lacks. Power users who want deep customization typically favor Zotero.
When Mendeley still makes sense
- You’re already embedded in the Elsevier ecosystem (Scopus, ScienceDirect)
- Your institution provides Mendeley support or training
- You’re in a field where most colleagues use Mendeley and you want shared group libraries
- You prefer a more polished out-of-box PDF annotation experience over extensibility
Related tools
- Zotero — open-source, community-maintained, stronger plugin ecosystem
- Semantic Scholar — for discovery; Mendeley does not replace literature search
- Elicit — for systematic extraction; Mendeley manages references but does not extract data