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Zotero has a built-in importer for Mendeley libraries, and for most people it is a single operation that preserves far more than an RIS export would. There are two things that catch people out: it works from your online library rather than the local one, and it will not touch group libraries.
Use the online import
In Zotero, go to File → Import and choose “Mendeley Reference Manager (online import)”. Zotero imports directly from your online Mendeley library, including the full folder structure.
Zotero’s documentation is explicit that your Mendeley password is never seen or stored by Zotero during this process.
Sync before you start — this is the step that fails
Because the import reads your online library, anything that has not reached Mendeley’s servers will not come across.
- If you use Mendeley Reference Manager, your data and files are already online.
- If you use Mendeley Desktop, check your sync settings to confirm that both data and files are syncing, and verify you can actually open your PDFs in the online library.
That last check is the useful one. “Sync is on” and “the PDFs are actually on the server” are different claims, and the import can only take what is there. Confirm in the web interface before importing, not afterwards.
What comes across
The import preserves considerably more than a bibliographic export:
- Item metadata
- Folders, which become Zotero collections
- Tags
- Notes
- Linked and stored files
- Extracted PDF annotations
The annotations matter. An RIS or BibTeX export carries none of them, so a “quick export” migration silently discards years of highlighting and margin notes while appearing to succeed. If you have annotated heavily, the importer is not merely more convenient — it is the difference between keeping and losing that work.
Group libraries do not import
It is not possible to import group libraries directly. The documented workaround is to copy the group items into a collection in your own Mendeley library first, then run the import.
Do this before you migrate, while you still have working Mendeley access. It is the most common thing people discover after they have already moved and stopped using the old tool.
Why there is no simple local import
If you have read older advice about importing from the local Mendeley database, it no longer applies to current versions, and the reason is worth knowing.
Per Zotero’s own account, work on a fully local importer began in early 2018, but a few months later Elsevier began encrypting the local Mendeley database, making it unreadable by Zotero and by standard database tools — despite Mendeley having previously promoted the openness of its database format as a guarantee against lock-in.
A local import route still exists but requires installing an old version of Mendeley Desktop, because later versions encrypt the database. Treat that as a fallback for people who genuinely cannot use the online path, not as the default.
A sequence that avoids rework
- Copy any group-library items you need into a collection in your personal Mendeley library.
- Confirm everything is synced — open several PDFs in the Mendeley web interface to prove files, not just metadata, are on the server.
- In Zotero: File → Import → Mendeley Reference Manager (online import).
- Spot-check after import: folder structure, a few annotated PDFs, and tags on items you know were tagged.
- Keep Mendeley installed and logged in until those checks pass. Do not cancel access on the same day you migrate.
Related
If you are still deciding, Zotero alternatives for researchers compares the main options, and Mendeley Reference Manager vs Mendeley Desktop explains which client you are actually running — which determines your sync situation above. Once migrated, running a systematic review library in Zotero covers structuring it for review work.
Frequently asked questions
Does Zotero import my PDF annotations?
Yes. Extracted PDF annotations come across, along with item data, folders, tags, notes and files. This is the main reason to use the importer rather than an RIS export, which carries none of them.
Do I import from the local database or online?
Online. Choose “Mendeley Reference Manager (online import)” and make sure everything is synced to Mendeley’s servers first.
Why can I not import from my local Mendeley files?
Elsevier began encrypting the local Mendeley database in 2018, which made it unreadable to Zotero and standard tools. A local route survives only via an older Mendeley Desktop version.
Will my Mendeley folders survive?
Yes — the full folder structure is imported and becomes Zotero collections.
What about group libraries?
They cannot be imported directly. Copy the group items into a collection in your own Mendeley library first, then import.
Does Zotero get my Mendeley password?
No. Zotero’s documentation states the password is never seen or stored.
References
- How do I import a Mendeley library into Zotero? — Zotero documentation
- Importing a Mendeley library into Zotero (alternative local method) — Zotero documentation
