In this paper, the authors have investigated the effects of different cleaning methods (centrifugation and dialysis) on the surface chemistry and composition of 15 nm sodium citrate stabilized gold nanoparticles. The nuclear magnetic resonance (NMR) results indicate that three centrifugation cycles are sufficient to remove most of the citrate molecules, while centrifuged liquid sedimentation and dynamic light scattering data reveal some degree of nanoparticle aggregation when three centrifugation cycles are exceeded. Regarding the dialysis procedure, NMR analysis demonstrated that after nine cleaning cycles, the citrate concentration is comparable to that measured after the first centrifugation (about 6 × 10−4 M) but with an increase in the dispersion polydispersivity index as determined by dynamic light scattering. X-ray photoelectron spectroscopy results support the NMR findings and revealed a major hydrocarbon contamination after the nanoparticles cleaning process. The impact of cleaning on surface functionalization was tested using 1H,1H,2H,2H-perfluorodecanethiol hydrophobic thiols (PFT) to test thiol-citrate substitution. After 24 h exposure, the PFT coverage was less than 0.6 monolayer (ML) for both pristine nanoparticles and particles after three dialysis cycles, but about 0.8 ML after two centrifugation washes.