A class of mesoporous silica material, FDU-12, was synthesized with different pore sizes and amine functionalized to determine its potential to differentially adsorb and separate dairy proteins. The adsorption behavior of the dairy proteins α-lactalbumin and β-lactoglobulin on the amino surface functionalised and unfunctionalised material was examined. It was shown that the pore size of unfunctionalised FDU-12 is an important factor in the protein adsorption capacity. Amine functionalization of FDU-12 significantly increased protein adsorption for larger pore size materials, with a marked difference in the rate of uptake between the two proteins. The kinetics of adsorption were investigated as a function of temperature and were modeled using pseudo second order kinetics and an intraparticle diffusion model, showing that intraparticle protein diffusion can be rate limiting. These results indicate that functionalised FDU-12 has potential for the selective separation of proteins with similar size and isoelectric point, under dynamic processing conditions.