The short answer: if you want a drop-in replacement for Zotero, look at Mendeley or Paperpile, and pick Paperpile if you write in Google Docs. If the real problem is that your references live in one app and your draft lives in another, no reference manager fixes that, because the split is the category. note.md is a macOS app that holds the PDFs, the highlights, the citations and the writing in one window.
What Zotero gets right
Zotero has been free and open since 2006 and it has earned the install base. The CSL style library covers essentially every journal you will ever submit to. The browser connector grabs metadata off a publisher page in one click and gets it right more often than anything else. Group libraries make shared reading lists genuinely easy. Since version 6 it has a competent built-in PDF reader with annotations, which closed the biggest gap it used to have.
None of that is what people complain about. The complaint is what happens after the reading.
Where the workflow breaks
You read a paper in Zotero and highlight the paragraph that matters. Then you open the app where you actually write. Now the highlight is over there and the sentence is over here, and getting one to the other means an export, or a plugin, or a copy and paste that strips the context. Three months later you are checking a claim before submission and the citation in your draft tells you the paper but not the page, so you open the PDF and start hunting.
That gap is where most of the friction in a literature review actually lives. It is also the thing an extra reference manager cannot close, because it sits between two apps rather than inside either one.
note.md closes it by refusing the split. A citation created with /cite points at the bookmark, not just the paper. Click it in November and the reader opens on the passage you highlighted in March, with the note you wrote at the time still attached.
Zotero and note.md, feature by feature
| Zotero | note.md | |
|---|---|---|
| Platforms | macOS, Windows, Linux, plus iOS | macOS only |
| Price | Free, paid storage tiers for sync above 300MB | Free. Premium for the local-AI features |
| Citation styles | Thousands, via CSL. Two decades of them | BibTeX and APA export |
| Word and Google Docs plugin | Yes | No. Export a .bib and cite in LaTeX, or write in note.md |
| Built-in PDF reader | Yes, with annotations | Yes, side by side with the editor |
| Notes | Yes, per-item and standalone | A full markdown writing environment, not a notes field |
| Linked notes and graph | No | Wiki links, backlinks and a graph view |
| Citation anchored to a passage | Annotation lives in Zotero; the citation in your draft points at the paper | The citation points at the specific bookmark and reopens it |
| Search by meaning | Keyword and full text | Local semantic search across every indexed passage |
| Where your library lives | On disk, synced through Zotero's servers or your own WebDAV | A folder on your Mac |
| Importing an existing library | Reads BibTeX, RIS, RDF and most competitors' exports | Not supported yet. Drag the PDFs in and metadata is read from the files. Zotero export import is on the roadmap, no date |
Moving a library across, and what that costs today
Be clear about this one before you get attached to the idea: note.md cannot import a Zotero export yet. No .bib import, no RDF, no collection structure. It is on the roadmap and being worked on, but there is no date, and you should make your decision on what the app does today rather than what it might do later.
What does work is dragging the PDFs themselves into Knowledge Management. note.md reads the metadata out of each file, so titles, authors and years mostly arrive on their own and you correct what it gets wrong. For a folder of papers that is a perfectly reasonable afternoon. For a decade-old library with collections, tags and hundreds of Zotero notes, it is not, and pretending otherwise would waste your weekend.
So the honest advice is the boring one. Leave finished projects where they are. Start the next chapter, or the next review, in note.md and see whether the single window is worth it before you think about moving anything. If it is not, you have lost an afternoon rather than a migration.
Two things worth knowing either way. Zotero reader annotations live in Zotero’s own database rather than inside the PDF, so highlights you made before the switch stay in Zotero regardless of how the import question is answered. And note.md exports a standard .bib, so whatever you build inside it can leave again.
