Using Zotero and Paperfy together:add AI summaries and audio review to citation management

Let's be clear from the start: this is not an article about switching away from Zotero.

Building bibliographies, inserting citations in Word, managing bibliographic records—Zotero and EndNote are the best at this, and Paperfy does not replace them here (it has no bibliography feature). The question runs the other way: how do you fill the gaps Zotero was never meant to cover?

Why do papers filed in Zotero end up unread? Because filing takes seconds while understanding takes the better part of an hour. That asymmetry is the whole problem.

What you need is a grip on the key points before reading (is this paper worth my time?), the figures at hand while reading, and review after reading. Layer understanding and review on top of the storage layer—that layer is what Paperfy is for.

Here's the concrete process.

One: when you find a paper, file it in Zotero as usual—Zotero remains the source of truth for bibliographic data. Two: upload the PDFs you intend to read carefully to Paperfy as well. Three: use Paperfy's AI summary for the big picture, reading against the original PDF and figures. Four: fold your insights and corrections into the summary as your record of understanding. Five: when you write, insert citations from Zotero.

Not every paper needs to be in both. Papers you might cite go in Zotero; papers you actually read go in Paperfy. Split it that way and the burden of running two libraries all but disappears.

Two tools for one literature collection sounds like duplicated effort. But look at what each tool actually holds—the information barely overlaps.

Zotero holds bibliographic data and the organization that serves citation. Paperfy holds AI summaries, figures, your personal notes, and review audio. The only overlap is the PDF file itself; the information being managed doesn't overlap at all. Owning both a refrigerator and a stove isn't duplicate kitchen management—it's the same idea.

Every paper you bring into Paperfy gets its own page. Because the AI summary is hand-editable, the corrections you make after checking the original accumulate as research notes.

You can turn finished papers into radio audio and review them on your commute, or rework a summary for a journal club and rehearse it by ear. If Zotero's library is a warehouse of citations, Paperfy's library is a workshop for understanding.

Even inside a combined workflow, the principle holds: the AI summary is the entry point, and the original PDF is the evidence.

Verify every cited number and conclusion in the original text, and correct the summary's misreadings by hand. Only when Zotero's accurate bibliography meets the accurate understanding you've built in Paperfy is a paper truly ready to be written about.

Adopting this workflow requires no changes on the Zotero side. Starting today, just add the papers you actually plan to read to Paperfy.

Try it first with one paper from this week's reading list.