Bacteriorhodopsin (BR) is a robust trans-membrane protein that functions as a light-driven proton pump, thus is an excellent candidate for biophotonics applications. For the development of new optical devices, the buildup of stable BR matrices has to be optimised. In this work, we present a multi- technique approach: the combination of optical waveguide lightmode spectroscopy (OWLS), atomic force microscopy (AFM) and multi-photon microscopy (MPM) aiming to analyze the optical and physico-chemical properties of BR embedded in polyelectrolyte multilayers (PEM) in its membrane bound form (purple membrane, PM), as well as solubilized BR immobilized within a photonic structure built of porous silicon (PSi). OWLS measurements revealed the possibility of incorporation of PM-BR layers into PE-multilayers. The calculated thickness and refractive index of the adsorbed layers demonstrate the successful adsorption of PM on top of the positively or negatively charged PE layers. Morphological studies by AFM proved a complete coverage of the positively charged PE layer with PM patches. As for the other model system, photonic responses of BR, after being immobilized within PSi substrates, have been evaluated using multi-photon microscopy. Fluorescence emission and second harmonic generation (SHG) of the BR-PSi system were observed at some particular pores of PSi and subsequent enhancement of the signal arising from the BR adsorbed within the pores was detected. Our results constitute the first steps of two interesting and innovative biomimetic approaches for the future design and development of BR based integrated optical devices.