The development of industrial biotechnology for an economical and ecological conversion of renewable materials into chemicals and fuels requires new strategies and concepts for bioprocessing. Biorefinery has been proposed as one of the key concepts with the aim of completely utilizing the substrate(s) and producing multiple products in one process or at one production site. In this article, we argue that microbial consortia can play an essential role to this end. To illustrate this, we first briefly describe some examples of existing industrial bioprocesses involving microbial consortia. New bioprocesses under development which make use of the advantages of microbial consortia are then introduced. Finally, we address some of the key issues and challenges for the analysis and engineering of bioprocesses involving microbial consortia from a perspective of biosystems engineering.