Immobilization of biological macromolecules, such as protein, onto solid supports is an important method for diagnostic assays andgenetechnology. This present study reports the size-selective adsorption/removal of virtual proteins that have different shapes, sizes, functions, and properties, such as insulin, cytochrome c, lysozyme, myoglobin, β-lactoglobin, α-amylase, hemoglobin, and myosin in aqueous water using mesobiocaptor monoliths. To prevent large proteins from adsorbing and remaining attached to adsorbent surfaces, large, open, cylindrical-pored, three-dimensional cubic aluminosilica mesostructures with large aluminum contents and micrometer-sized monolith particles were fabricated. The unique physical properties and the surface functionality of the mesobiocaptors enhance protein adsorption characteristics in terms of loading capacity and quantity of the sample, ensuring a higher concentration of adsorbed proteins, interior pore diffusivity, and encapsulation in a short period. Thermodynamic studies indicate that protein adsorption into the mesobiocaptor pores is favorable and spontaneous. Theoretical models were used to investigate the major driving forces for the most optimal performance of the protein adsorption. The geometrical findings point to key factors, such as surface energy, intermolecular forces, charge distribution, hydrophobicity, and electrostatic interaction, which might control the adsorption into the interior large, open cylindrical mesobiocaptor cavities (sized 3–16 nm) without aggregation of these proteins on the exterior surfaces of monoliths. Indeed, the availability of adsorption of single proteins from mixtures based on size- and shape-selective separation opens new avenues of research in encapsulation of proteins and bioanalysis.