Immobilization of free enzymes/proteins on water-insoluble mesoporous silica (MS) supports is often applied to obtain efficient biocatalysts for various applications. Three methods were applied for enzyme bonding onto MS: (1) physical adsorption with subsequent crosslinking of enzymes, (2) adsorption on aminated MS with subsequent crosslinking of enzymes, and (3) covalent bonding using MS, the surface of which was modified using oxirane or amino groups provided by various organosilanes. The measurements included: determination of activity of freely suspended enzymes and of those attached to different carriers, measurements of protein loading, and determination of biocatalysts stability (both operational, at most real situations, and after one month storage). The results obtained clearly indicate that activity of the aminated MCF-based biocatalysts is significantly higher than of both SBA-15-based counterparts, and it is often an order of magnitude higher than of the preparations fabricated using recommended procedures and conventional supports. The protein loading, while being an important factor, has not been found critically significant. The microenvironment of proteins and porous texture of supports emerge as far more important factors and here the unique properties of the modified MS in general, and MCFs in particular, can hardly be matched.