Since phytoplasmas cannot be cultured in vitro, it is impossible to study a protein of interest in vivo by manipulating its corresponding gene. It is therefore necessary to recombinantly express a protein of interest for use in an in vitro study. Although recombinant expression of proteins in E. coli is well established, there are some issues to consider when expressing recombinant phytoplasma proteins. Here, we describe a detailed method for the recombinant expression of an effector protein, SAP11, from ‘Candidatus Phytoplasma mali' in E. coli. Some important points are highlighted.