Encapsulation of several biologically important proteins, cytochrome c, catalase, myoglobin, and hemoglobin, into transparent porous silica matrices by an aqueous colloidal sol–gel process that requires no alcohol is reported. Optical characterization indicates a successful retention of protein conformation after encapsulation. The conformation retention is strongly correlated to both the rate of gelation and the subsequent drying speed. Using hemoglobin as a model protein, a higher colloidal solid concentration and a lower synthesis pH were found, both causing faster gelation, resulting in a better retention of conformation. Hemoglobin encapsulated in a thin film, which dries faster, also showed a better retention than in the bulk. This is attributed to the fact that when a protein is isolated, and especially when it is confined to a space close to its own dimensions, conformational changes are sterically hindered, hence the structural stability. Enzymatic activity of bovine liver catalase was also monitored and showed a remarkable improvement when encapsulated using the aqueous colloidal process, compared to using the conventional alkoxide-based process. Thus, the aqueous colloidal sol–gel process offers a promising alternative to the conventional sol–gel process for encapsulating biomolecules into transparent, porous matrices.