The immobilization of biological species such as proteins and enzymes in sol-gel hosts is currently an area of intense research activity. However, the majority of these studies have been directed toward investigating the biological activity or physicochemical properties of the encapsulated species, with much less attention having been directed toward the effect of proteins on the structural evolution of the sol-gel matrix. This study investigates the structural evolution of sol-gel matrices in the presence of a model protein, bovine serum albumin (BSA). The sol-gel matrices were produced via the NaF-catalyzed hydrolysis of a mixture of tetramethyoxysilane (TMOS) and methyltrimethoxysilane (MTMS), yielding nanohybrid matrices with controlled pore sizes, pore volumes, and surface chemistry. The structural evolution of the matrix was investigated using a complementary suite of techniques, including solid-state (29)Si NMR, FTIR, SANS contrast variation, and N(2) sorption. A novel approach was developed to model the SANS data, to extract key structural parameters. The results indicated that the structural evolution of the matrices was modulated by a series of complex interactions between the enzyme and the evolving sol-gel nanohybrid: On the molecular scale, increasing BSA content led to an associated increase in both the abundance of linear Si-O-Si species (FTIR) and the Qn network connectivity ((29)Si NMR). However, only minor changes in the connectivity of the evolving Tn network were evident with varying BSA content. The selective role of the protein in these systems, where the approach of the methylated monomer to the vicinity of the protein's surface is presumably impeded by the hydrophobicity of the monomer, will be discussed. On the nanoscale, N(2) sorption data were consistent with an initial increase in the mesopore volume and surface area at low BSA loadings, followed by a subsequent monotonic decrease with increasing BSA content. In contrast, no such trends were evident in the in situ SANS data obtained from these samples, suggesting that modulation of the evolving network structure of the silica matrix by BSA during condensation prevents collapse of the nanoscale gel structure during freeze-drying. This latter comparison reflects the important role of in situ techniques such as small angle scattering (which can be used to study both open and closed porosity and probe nanostructure on length scales from approximately 1 nm to >100 nm) in investigating such complex, multicomponent systems, and techniques for modeling such data in sol-gel systems will be discussed.