Sarcoplasmic reticulum (SR) membranes from rabbit muscle were deposited on silicon substrates and characterized by the combination of spectral ellipsometry (SE), high energy specular X-ray reflectivity (XRR), specular neutron reflectivity (NR), and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. Following the optimization of the preparative conditions by SE, the detailed structures in the direction perpendicular to the membrane were probed by XRR. ATR-FTIR data showed strong signals from amide I and amide II bands of the native SR membranes containing a large amount of Ca2+-ATPase, which could not be achieved by the reconstitution in artificial lipid membranes. The treatment with protease led to a significant decrease in the amide peaks, and the XRR data confirmed the modulation of the membrane structures. The obtained data show the potential of the in situ combination of reflectivity and vibrational spectroscopy of native supported membranes in order to unravel both structure and dynamics of complex biological membranes.