A wide range of hybrid biomaterials has been designed in order to sustain bioremediation processes by associating sol-gel SiO2 matrices with various biologically active compounds (enzymes, antibodies). SiO2 is a widespread, chemically stable and non-toxic material; thus, the immobilization of enzymes on silica may lead to improving the efficiency of biocatalysts in terms of endurance and economic costs. Our present work explores the potential of different hybrid morphologies, based on hollow tubes and solid spheres of amorphous SiO2, for enzyme immobilization and the development of competitive biocatalysts. The synthesis protocol and structural characterization of spherical and tubular SiO2 obtained by the sol gel method were fully investigated in connection with the subsequent immobilization of lipase from Rhizopus orizae. The immobilization is conducted at pH 6, lower than the isoelectric point of lipase and higher than the isoelectric point of silica, which is meant to sustain the physical interactions of the enzyme with the SiO2 matrix. The morphological, textural and surface properties of spherical and tubular SiO2 were investigated by SEM, nitrogen sorption, and electrokinetic potential measurements, while the formation and characterization of hybrid organic-inorganic complexes were studied by UV-VIS, FTIR-ATR and fluorescence spectroscopy. The highest degree of enzyme immobilization (as depicted from total organic carbon) was achieved for tubular morphology and the hydrolysis of p-nitrophenyl acetate was used as an enzymatic model reaction conducted in the presence of hybrid lipase–SiO2 complex.