Spectroscopic ellipsometry (SE) has been used to investigate the adsorption of yeast cytochrome c (YCC) on gold films. YCC is a prototypical molecular system to evaluate the sensitivity and reliability of optical methods in probing conformational changes upon adsorption at surfaces. Measurements have been performed in situ in aqueous solutions at room temperature. We have applied to monolayer-thick YCC films the same scheme of analysis of SE spectra used in our recent works on thiolate self-assembled monolayers on gold, exploiting the so-called δ and δ difference spectra. A comparison between δ and δ spectra obtained from YCC adsorption on flat and cluster-assembled nanostructured gold films, obtained by supersonic cluster beam deposition is proposed. For both kinds of substrate δ and δ , difference spectra show well-defined features related to molecular optical absorptions typical of the so-called heme group, in particular the Soret band at about 410 nm. These features appear in the same position found for molecules in solution, suggesting that YCC native conformation is maintained upon adsorption also in the case of a substrate with typical roughness at the nanoscale.