I use rmarkdown which has native citation support (I think part of pandoc)
https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html
I save my citations to Zotero then export to bibtex
Each citation entry has a name like @titletext1_titletex2_author1_author2_year
I can then directly reference citations in the markdown by referring to the @bibtex_id