A comprehensive study on the general functionalization strategies for magnetic nanoparticles (MNPs) is presented in this work. Using well-established techniques as well as modified protocols, the wide range of functional moieties grafted on γ-Fe2O3 (maghemite) nanosurfaces include those of amine, aldehyde, carboxylic, epoxy, mercapto, and maleimide ends. Among the modified protocols are the one-step water-catalyzed silanization with mercaptopropyltrimethoxysilane, resulting in dense distal thiols, and the direct functionalization with a heterogeneous bifunctional linker N-[p-maleimidophenyl]isocynanate (PMPI). The former results in a protective Stöber type coating while simultaneously reducing the iron oxide core to magnetite (Fe3O4). The conjugation of trypsin, hereby chosen as model biomolecule, onto the differently functionalized MNPs is further demonstrated and assessed based on its activity, kinetics, and thermo-/long-term stability as well as reusability. Besides aqueous stability and ease in recovery by magnetic separation, the immobilized trypsin on MNPs offers superior protease durability and reusability, without compromising the substrate specificity and sequence coverage of free trypsin. The MNP-based proteases can be used as valuable carriers in proteomics and miniaturized total analysis devices. The applicability of the functional surfaces devised in the current study is also relevant for the conjugation of other biomolecules beyond trypsin.