Cellular metabolic pathways are paradigms for the rapid and waste-free conversion of molecules into useful products through multiple enzyme-catalyzed steps (cascade reactions). Attempts to establish efficient cascade reactions for technological applications have focused on mimicking nature's high degree of organization by controlling the positioning of enzymes through immobilization in tailor-made compartments. The present work utilized peptide-mediated layer-by-layer mineralization as a facile and generic method for the compartmentalisation of multi-enzyme systems in nanoscale silica layers. It is demonstrated that, in a multilayer system, the overall rate of the reaction cascade was primarily affected by the placement of the enzyme catalyzing the first step, with the placement of the enzyme possessing the lowest catalytic efficiency also being an important factor. As the rate-limiting enzymes were positioned closer to the external silica surface, the overall rate of cascade reactions increased. Furthermore, distributing the enzymes into different adjacent silica compartments yielded higher overall cascade reaction rates compared to placement of the enzymes into the same silica layer. The synthetic methods and kinetic analyses presented here provide guidance for improving the performance of immobilized multi-enzyme systems for a wide range of technological applications.