With a first commercial biopharmaceutical product on the market, and other products proceeding through clinical development stages, the concept of plant molecular farming has proven a viable alternative to traditional production platforms. To extend the range of target molecules amenable for molecular farming, there is constant ambition to tailor the current plant host systems to improve the quality of the final product. These efforts have been focused mainly on glycan engineering, as the majority of target molecules are glycoproteins. In the past few years also more research addressed proteolytic processing of recombinant target molecules and strategies have been devised to protect valuable target proteins from degradation. Recent developments in these areas as well as in downstream processing including extraction and purification processes will be discussed.