We report herein two methods to characterize the surface of mixed-ligand shell gold nanoparticles, which was explored with gold nanoparticles containing varying molar ratios of 3-mercaptopropionic acid (MPA) and 3-mercapto-1-propanesulfonate (MPS) or 11-mercaptoundecanoic acid (MUA) and triethylene glycol mono-11-mercaptoundecyl ether (TEG) in their ligand shell. Incubation of gold nanoparticles with a solution containing the transition metal cation Ni2+ allows the extraction of Ni2+ depending on the number of negatively charged surface groups and the reaction of surface carboxylic acid groups with an aminomethyladamantane derivative allows the extraction of the supramolecular host molecule cucurbituril (CB7) depending on the number of reactive surface groups. In both the methods, the remaining surface probes in the supernatant could be conveniently quantified in a homogeneous solution after a simple centrifugation step. An excellent linear correlation between the amount of Ni2+ extracted and the ligand density of MPA and MPS in MPA/MPS gold nanoparticles or MUA in MUA/TEG gold nanoparticles afforded a simple and reliable assay method to determine the number of negatively charged surface groups. The supramolecular CB7 assay enabled the determination of the accessible ligand density of reactive surface carboxylic acid groups and revealed a striking difference in the number of surface groups that can be reacted with MPA/MPS gold nanoparticles or MUA/TEG gold nanoparticles, which suggests a simple method to probe the surface structure of mixed monolayer gold nanoparticles.