Zettlr

Zettlr is a markdown editor for people whose writing has a bibliography. Point it at a Zotero export or a .bib file and citation keys autocomplete as you type, render as readable references while you write, and come out the other side correctly formatted through Pandoc. It also does the Zettelkasten things — internal links between notes, tags, full-text search across a folder — but the citation handling is why people pick it over a general markdown app.

Everything lives as plain files in directories you choose. There is no account, no tier and no cloud component. The project is free and open source, funded by donations, and has been maintained by Hendrik Erz since 2017.

The setup cost is real and worth knowing before you start. Export beyond HTML needs Pandoc installed, and PDF output needs a LaTeX distribution on top of that, which is a multi-gigabyte download and an afternoon the first time. Zettlr will not do that part for you. It is also an Electron app, so it sits heavier in memory than a native editor, there is no mobile version, and sync is whatever you arrange with iCloud Drive or git.

If you are writing a thesis or papers and were about to pay for a reference-managing writing suite, start here before spending anything. If you write fiction or general notes, the citation machinery is weight you will never use.