Mendeley is a free reference manager that systematic reviewers use to import the records from their database searches, build and organise a library of references and attached full-text files, remove duplicates, insert citations into a manuscript through a word-processor plugin, and export a clean set to a screening tool. The current product is the Mendeley Reference Manager, which replaced the older Mendeley Desktop, and it sits in the reference-and-tidy stage of a review rather than the blinded screening stage that a dedicated platform handles.
Where Mendeley fits in a review
Every systematic review searches more than one database, so all of those records have to be gathered in one place before screening. Mendeley is built for that consolidation and for the writing that comes later: bring in each export, deduplicate, organise the library, then export the unique records to a screening tool and, at the end, cite the included studies in the manuscript. It is the reference layer, not the decision layer, because Mendeley has no built-in way to run two blinded reviewers or to resolve their conflicts. Knowing that boundary keeps the workflow clean; the blinded decisions happen in a dedicated tool after the library leaves Mendeley, as our overview of systematic review screening tools explains.
Building and organising a library
Mendeley imports the standard formats databases produce, including RIS and other tagged exports, and its browser importer can save records straight from a results page. Inside the library you organise references with folders and can add notes, so a practical review setup is one folder per database for the raw imports and a combined folder for the deduplicated set, which keeps the source of each record traceable. Keeping the original export from each database is part of properly documenting a search strategy, and a folder structure that mirrors your sources makes that record easy to maintain. As with any reference manager, the folders organise references; they do not stand in for the formal eligibility decisions a screen records.
Deduplication in Mendeley
Mendeley can detect and merge likely duplicates within a folder, matching on fields such as title, authors, and year, and letting you confirm each merge. It handles the obvious cases well, but like other reference managers it is cautious about the awkward ones, so it can miss near duplicates where punctuation, accents, or a truncated title differ between two exports. The reliable habit is to run the automated merge and then scan the remainder by hand, because wrongly deleting a unique study here is invisible later; the same principles apply across tools and are set out in our guide to deduplicating search results.
The citation plugin for Word
Mendeley installs a citation plugin, the Mendeley Citeadd-in, into your word processor so you can insert in-text citations and build a reference list directly from your library while you write. The flow is straightforward: place the cursor, search your library from the add-in pane, insert the citation, and let the tool generate and update the bibliography in your chosen style. Changing the citation style restyles every reference at once, which matters for a review manuscript that may move between target journals. This writing-stage support is one of Mendeley’s strengths, and it is the part of the workflow that comes after the search, screening, and data extraction are complete.
The discontinuation of Mendeley Desktop
For years the main application was Mendeley Desktop, and many long-time users still think of it as “Mendeley”. It has been discontinued in favour of the newer Mendeley Reference Manager, a rebuilt application with a different interface and a revised feature set. The change caught some users out, because a few features they relied on behaved differently or moved, and it prompted a number of reviewers to reassess their reference manager altogether. If you are returning to Mendeley after a gap, expect the current application rather than the old one, and check that the features your workflow depends on are present before committing a live review to it.
Exporting a clean library to a screening tool
The hand-off from Mendeley to the decision stage is the step reviewers most often fumble, so it is worth doing deliberately. Once the combined folder holds the deduplicated set, select those references and export them in a format the screening tool accepts, almost always RIS or a tagged text export, and check that the fields you rely on for screening survive the transfer: the title, the abstract, the authors, the year, and the digital object identifier. A common failure is an export that drops the abstract, which leaves screeners working from titles alone and quietly inflates the number of full texts they have to retrieve. Run a small test export of a dozen records, open it in the screening tool, and confirm the abstracts came through before you move the whole library. It also pays to export once and screen once, because re-exporting a changed library midway through title and abstract screening can reintroduce records you have already excluded. Treat the exported file as a fixed snapshot, record how many references it contained, and that count becomes the screened figure in your flow diagram.
How Mendeley compares with Zotero
Mendeley and Zotero are the two leading free reference managers, and the choice between them is close. Both import the standard formats, organise a library, deduplicate, attach full-text files, and cite in a word processor. Zotero is open source and community-governed, which appeals to reviewers who want an independent tool, and it is strong on flexible tagging and saved searches. Mendeley benefits from being part of a larger publishing platform and pairs naturally with its citation add-in. For systematic review work the differences are smaller than the similarities, and either can carry the reference workload for a small to mid-sized review before the records move into a screening tool. If you want the detail on the open-source option, see our guide to using Zotero in a review workflow, and for the wider field, including the paid heavyweight, our comparison of the main citation managers lines all three up side by side.