The formation of structured protein–silica composite assemblies is described. The assemblies were prepared using a convenient one step sol–gel technique developed in our group, from which porous silica particles, films or monoliths can be synthesized. Two biomolecules were used, bovine serum albumin (BSA) and lysozyme, to modify the porous structure of the as-synthesized silica materials. The composite materials were characterized using scanning electron microscopy, N2 sorption isotherms, FT-IR spectroscopic data, differential scanning calorimetry and thermal gravimetric analysis. The existence and nature of interactions between the proteins and the silica in the as-synthesized composite materials were investigated using FT-IR, particularly with respect to the conformation of the proteins. The conformation of both proteins is modified upon occlusion into the silicate network with a reduction in the extent of α-helices resulting in a more disordered state. In the case of BSA the presence of β-sheets is detected. Both BSA and lysozyme establish H-bonding and electrostatic interactions with the silica. Protein concentrations in the range of 2 to 8 mg mL−1 of condensing solution were investigated. Upon variation of the concentration of proteins, nitrogen adsorption data and SEM investigation confirm that, the bimodal porous structure and the uniform pore size distribution is maintained in the as-synthesized composite materials for all protein concentrations used. Both the as-synthesized and fully calcined (water and organic components removed) materials show bimodal porosity of ∼2 μm and ∼52 nm (BSA additive) and ∼5 μm and ∼57 nm (lysozyme additive). The sizes of both the nanometre and micrometre sized pores are slightly reduced in the presence of protein as compared to materials synthesized with no protein due to the interactions between the biomolecules and the silica.