Continuous-flow processing in the manufacturing of modern biotherapeutics represents a great potential and could significantly improve productivity and product quality as well as reduce operating costs. Microfluidic perfusion systems are not only capable for producing therapeutic proteins but also suitable for organ-on-a-chip based drug testing and toxicology studies. Integrating modular unit operations for protein purification in the microfluidic cell culture device can lead to point-of-care therapeutic protein production. The multi-organ microfluidic platforms that integrate several organ-on-a-chip microfluidic units will help in preclinical testing of drug substances and toxicological studies by producing highly reliable preclinical pharmacokinetic data. In this perspective, the current state of the art and future trends of continuous flow systems are summarized for biopharmaceutical production and organ-on-a-chip drug testing.