Systems of co-immobilized microorganisms are highly effective for conducting two or more consecutive bioprocesses within close proximity of the source and the sink of substrates. In this work, a general model of a co-immobilized aerobic/anaerobic bacterial system was developed and analyzed. The model was used to optimize pellet design and to study the effect of slow cell growth on process efficiency. The analysis demonstrated that co-immobilization of bacterial species accelerates the rate of biotransformation and provides complete transformation of toxic intermediates.