Mesoporous materials bear great potential for biotechnological applications due to their biocompatibility and versatility. Their high surface area and pore interconnection allow the immobilization of molecules and their subsequent controlled delivery. Modifications of the mesoporous material with the addition of different chemical species, make them particularly suitable for the production of bioactive coatings. Functionalized thin films of mesoporous silica and titania can be used as scaffolds with properties as diverse as promotion of cell growth, inhibition of biofilms formation, or development of sensors based on immobilized enzymes. The possibility to pattern them increase their appeal as they can be incorporated into devices and can be tailored both with respect to architecture and functionalization. In fact, selective surface manipulation is the ground for the fabrication of advanced micro devices that combine standard micro/nanofluids with functional materials. In this review, we will present the advantages of the functionalization of silica and titania mesoporous materials deposited in thin film. Different functional groups used to modify their properties will be summarized, as well as functionalization methods and some examples of applications of modified materials, thus giving an overview of the essential role of functionalization to improve the performance of such innovative materials.