In the Pandoc Plugin settings, add — citeproc to the ‘Extra Pandoc arguments’ setting. This will be what takes the markdown citations and converts them to in-text citations in the conversion process. It also inserts a full reference list on the end of your document automatically, all completely formatted. To get this to work, you have to specify the location of the .bib file on your system by adding the path, in quotations, to a ‘bibliography’ YAML property.