Driven by many applications, the development of new biomaterials has considerably increased in the last decade. The current research strategies also involve revealing of the relationship between protein structure and function due to the exposure and interaction of proteins with non-biological organic and inorganic solid surfaces. Aiming at understanding of the mechanisms of protein adsorption on solid surfaces we follow in this work the organization dynamics of proteins (Bovine Serum Albumin, BSA and Fibronectin, Fn) adsorbed on thin silica layers without or with silver nanoparticles (AgNPs), deposited on their surfaces. It is found that although starting with the same protein concentration in solution (0.05 g/L), the adsorbed amount of proteins on SiO2 surfaces is twice larger for Fn (1.32 µg/cm 2) compared to BSA (0.58 µg/cm 2). The proteins adopt different conformations according to the surface pattern. On a flat SiO2 surface, the BSA proteins organize in a lace-like network while the Fn proteins adopt a branching-type. The patterned by AgNPs surfaces induce conformational changes of the proteins. In interaction with AgNPs both types of proteins fold up to attain mainly compact globular conformation.