Lysozyme-templated precipitation of silica synthesized by sol-gel chemistry produces a composite material with antimicrobial properties. This study investigates the structural properties of the composite material that allow for retention of the antimicrobial activity of lysozyme. Scanning (SEM) and transmission (TEM) electron microscopy reveal that the composite has a hierarchical structure composed of quasi-spherical structures (∼450 nm diameter), which are in turn composed of closely packed spherical structures of ∼8–10 nm in diameter. Using small-angle neutron scattering (SANS) with contrast variation, the scattering signatures of the lysozyme and silica within the composite were separated. It was determined that the lysozyme molecules are spatially correlated in the material and form clusters with colloidal silica particles. The size of the clusters determined by SANS agrees well with the structural architecture observed by TEM. BET analysis revealed that the surface area of the composite is relatively low (4.73 m2/g). However, after removal of the protein by heating to 200 °C, the surface area is increased by ∼20%. In addition to demonstrating a well organized sol-gel synthesis which generates a functional material with antimicrobial applications, the analysis and modeling approaches described herein can be used for characterizing a wide range of mesoporous and ultrastructural materials.