AbstractThis article presents the fusion of two hitherto unrelated fields—microbioreactors and topology optimization. The basis for this study is a rectangular microbioreactor with homogeneously distributed immobilized brewers yeast cells (Saccharomyces cerevisiae) that produce a recombinant protein. Topology optimization is then used to change the spatial distribution of cells in the reactor in order to optimize for maximal product flow out of the reactor. This distribution accounts for potentially negative effects of, for example, by‐product inhibition. We show that the theoretical improvement in productivity is at least fivefold compared with the homogeneous reactor. The improvements obtained by applying topology optimization are largest where either nutrition is scarce or inhibition effects are pronounced. Biotechnol. Bioeng. 2011; 108:786–796. © 2010 Wiley Periodicals, Inc.