Gold nanoparticles (AuNPs) are attractive materials due to their special optical and electronic properties. However, they tend to aggregate particularly in the presence of thiol‐containing compounds. In this study, to investigate the effect of surface conjugation with thiol‐containing compounds on colloidal stability, thiol compounds with various structures as modifying agents were used. To this end, AuNPs were synthesized and stabilized by trisodium citrate in aqueous solution, and then modified with thiol‐containing compounds, namely cysteamine hydrochloride (MEA, containing primary amine groups), 2‐mercaptoethanol (BME, containing hydroxyl groups), 1‐dodecanthiol (LCA, containing long‐chain alkyl groups) and thioglycolic acid (TGA, containing carboxylic acid groups). We studied the effect of thiol ligands on solution stability of colloidal AuNPs and on the formation of aggregates originating from the modification process using UV–visible spectroscopy, dynamic light scattering, field emission scanning electron microscopy and transmission electron microscopy. Results showed that surface modification with MEA, BME and LCA led to the formation of aggregates. However, conjugation with TGA showed a concentration‐dependent behaviour: surface modification with low concentration resulted in the formation of aggregates whereas that with high concentration of TGA did not disturb the colloidal stability of AuNPs. Finally, the effect of surface modification on temperature increase of solutions originating from infrared light irradiation was studied, where the temperature increase depends on the surface‐modifying compound.