Hybrid inorganic-organic materials comprising organic functional groups tethered from silica surfaces are versatile, heterogeneous catalysts. Recent advances have led to the preparation of silica materials containing multiple, different functional groups that can show cooperative catalysis; that is, these functional groups can act together to provide catalytic activity and selectivity superior to what can be obtained from either monofunctional materials or homogeneous catalysts. This tutorial review discusses cooperative catalysis of silica-based catalytic materials, focusing on the cooperative action of acid-base, acid-thiol, amine-urea, and imidazole-alcohol-carboxylate groups. Particular attention is given to the effect of the spatial arrangement of these organic groups and recent developments in the spatial organization of multiple groups on the silica surface.