Modification of metal surfaces with complex molecules opens interesting opportunities to build additional functionality into these surfaces. In this work, self assembled monolayers (SAMs) based on the same photoswitchable azobenzene motif but with different head groups have been synthesized and their SAMs on Au(111)/Si substrates have been characterized. 3-[(4-phenylazo)phenoxy]propyl thiol (PAPT) and its acetyl group protected analog, 3-[(4-phenylazo)phenoxy]propyl thioacetate (PAPA), have been synthesized. SAMs from PAPT and PAPA have been characterized by infrared (IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), ellipsometry and cyclic voltammetry (CV). The SAM-forming units of both SAMs are the same, as confirmed by IR and XPS, and the SAMs have similar surface coverage, as evidenced by analysis of the reductive desorption peaks in CVs. The tilt angle of the azobenzene moiety was ca. 75° with respect to the surface normal as determined by IR spectroscopy, i.e., the molecules are lying quite flat on the gold surface. Despite similar surface coverages, the CVs for PAPT in aqueous perchlorate solution show a typical perchlorate adsorption peak to gold, whereas the corresponding experiments with PAPA show no perchlorate adsorption at all. In conclusion, SAM formation can lead to an increase in the number of electrochemically accessible surface sites on the final, SAM covered surface. Whether the amount of such sites increases or decreases, depends on the precursor. The precursor most likely affects the adsorption mechanism and thus the atomic surface structure of the metal at the metal/SAM interface. Thus, details of the SAM formation mechanism, which is affected by the precursor used, can have quite strong effects on the electrochemical properties, and likely also electrocatalytic properties, of the resulting modified surface.