The aim of this work was to investigate the conformational changes and diffusion of adsorbed proteins (immunoglobulin G (IgG), fibrinogen (Fib) and human serum albumin (HSA)) on hydrophilic quartz and hydrophobized quartz (octadecyltrichlorosilane (OTS)) surfaces. Circular dichroism spectroscopy measurements have shown that IgG is the most stable protein after adsorption on hydrophilic quartz, whereas HSA and Fib unfold. The structural changes are dependent on adsorption time, initial protein concentration in bulk, and surface chemistry. The effect of trifluoroethanol (TFE) in recovering the original protein structure after adsorption was analyzed by total internal reflection fluorescence and fluorescence recovery after photobleaching (TIRF-FRAP). TIRF-FRAP experiments revealed a strong dependence of the surface chemistry on protein diffusion coefficients: proteins diffuse 4 times slower on hydrophobic surfaces than on hydrophilic surfaces. The diffusion coefficient of TFE at hydrophobic surfaces is 2 orders magnitude higher than at hydrophilic surfaces. However, protein desorption occurs faster on hydrophilic quartz than on OTS, proving that the strength of protein-surface interaction is weaker at hydrophilic surfaces. This result shows that desorption is determined by surface/protein chemistry and not by mass transfer limitations. FTIR-ATR results demonstrated that TFE interaction with adsorbed proteins is stronger at hydrophilic surfaces than at hydrophobic surfaces.