Large-pore mesoporous silica supports with different structure and pore sizes distribution have been tested for glyoxyl multipoint covalent immobilization of Pectinex Ultra SP-L, a commercial preparation including the enzyme β-galactosidase from Aspergillus aculeatus. The prepared biocatalysts have been assayed in the production of galacto-oligosaccharides (GOS) from lactose as prebiotic functional food, aiming to optimize the yield to the GOS having the highest presumed prebiotic effect, tri- and tetra- GOS (high-GOS). Immobilization of β-galactosidase over glyoxyl-modified silica supports, with pores, large enough to accommodate the enzyme within their structure, led to an enhancement of the enzyme activity in terms of high-GOS production relative to the free enzyme under the same reaction conditions. Remarkably, such an improvement was achieved without previous purification of β-galactosidase from the commercial source. An enhancement of the transgalactosylation activity over the hydrolytic activity, due to the relatively hydrophobic nature of organically modified silica surface of the supports, led to an increase in the selectivity to high-GOS. The best biocatalyst in the series was that based in hexagonal ultra-large-pore SBA-15 (ULP-SBA-15), which presents the most adequate balance between confinement effect within its pore framework and transgalactosylation activity leading to a remarkable yield to high-GOS of 20.2% vs. 11.2% for the enzyme in free conditions. Furthermore, reusability of these silica-based biocatalysts in three consecutive 24 h reaction-cycles has been successfully performed at 50 °C, temperature that minimizes the thermal deactivation of the enzyme.