The Photosynthetic membrane protein of bacteriorhodopsin (bR) was encapsulated in an optically transparent and porous silica matrix using a modified sol-gel procedure. The absorption spectra and the kinetics of the photocycle characteristic of the proton pumping function of bR were studied systematically throughout the different stages of the glass formation process. This new biomaterial was characterized by means of its optical absorption, circular dichroism (CD), and Raman spectra; its photocycle kinetics; the characteristic activation parameters of its photocycle; and its deionization and cation regeneration properties. The global trimeric bR structure, the local structure of the retinal chromophore, and the proton pumping function of bR were not affected by the encapsulation process. It was also found that the bR glass formed allowed transport of small ions such as Ca2+ in to and out of the glass medium, and those ions were found to affect the properties of the protein just as they do in aqueous suspensions. The bR protein was found to bleach if delipidated prior to encapsulation. These observations as well as analysis of the CD spectrum suggest that the bR is encapsulated along with its membrane lipids. These results taken together suggest that this optically transparent system offers a potentially useful new bR-containing material for optical imaging and optically based ion-sensoring devices as developed and proposed for other bR-based systems.