We study the effect of additives on the colloidal stability of alkanethiol-coated gold nanoparticles. Cyclic amines and sulfides of different sizes were added to dispersions in decane at additive concentrations below 128 mM. Small-angle X-ray scattering (SAXS) indicated that tetrahydrothiophene reduced the agglomeration temperature, Tagglo, by up to 29 °C, a considerable increase in colloidal stability. Amines had a much weaker stabilizing effect of up to 2.5 °C. We found an unexpected maximum of stabilization for low additive concentrations, where Tagglo increased at concentrations above 64 mM. Molecular dynamics simulations were used to correlate these observations with the ligand shell structure. They excluded the physisorption of additives as a stabilization mechanism and suggested that sulfides replace hexadecanethiol on the AuNP surfaces by chemisorption. This hinders ligand ordering, thereby reducing Tagglo, which explains the stabilizing effect. Clustering of chemisorbed additive molecules at high concentration restabilized the ligand ordered state, explaining the detrimental effect of higher additive concentrations. The predictions of the simulations were confirmed by using thermogravimetric analyses and SAXS measurements of washed samples that indicated that the structure of the ligand shell itself, not the presence of physisorbed additives, changes Tagglo. Finally, we calculated potentials of mean force, which show that larger sulfide-based additives have a weaker affinity for the gold surface than smaller ones due to stronger steric hindrance. This explains why smaller cyclic sulfides were the most efficient stabilizers.