Membrane technology has a wide range of applications in upstream and downstream bioprocessing of industrial products. Due to the increased interest in the development of continuous bioprocessing units, bioreactors coupled to a membrane separation process have been extensively assessed in the last decade, showing incredible potential for its application in food and pharmaceutical industries as well as energy production and environmental remediation. In this chapter, applications of membrane bioreactors in biotechnology processes are reviewed. Moreover, removal of recalcitrant pollutants (e.g., trace organic contaminants) by membrane bioreactors are critically analysed. Bottlenecks affecting the scale-up of membrane bioreactors in biotechnology processes are identified and discussed.