By functionalising gold samples, planar wafers or AFM tips, with an acid- or an amino acid-terminated thiols, mercaptoundecanoic acid (MUA) and homocystein (H-Cyst) respectively, we were able to differentiate the interactions with ammonium perchlorate (AP) and starch (S), two components of a nanocomposition mixture. To do so, the interaction between gold functionalized surfaces and the two targeted compounds have been characterized and quantified by several complementary techniques. Polarisation modulation-infrared spectroscopy (PM-IRRAS), and X-ray photoelectron spectroscopy (XPS), providing chemical analyses of goldsurfaces after contacting S or AP, proved that both compounds were retained on MUA or H-Cyst-modified surfaces, but to various extents. Quartz crystal microbalance on-line measurements enabled to monitor the kinetics of interaction and showed distinct differences in the behaviour of MUA and H-Cyst-surfaces towards the two compounds. Having observed that only H-Cyst-modified surfaces enables to get a contrast on the chemical force microscopy (CFM) images, this new result could be well explained by examining the data obtained by combining the above-mentioned surface characterisation techniques.