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.