We optimized a method for the preparation and purification of self-assembled protein nanocontainers EPN, the latest achievement in protein engineering. These nanocontainers are highly stable and provide the possibility of highly specific loading of a protein therapeutic drug. The described technique can be proposed as a tool for production of nanocontainers in a prokaryotic system. The obtained nanocontainers for the delivery of protein preparations can be used in the treatment of chronic, autoimmune, and oncological diseases.