The thermal stability of self-assembled monolayers (SAMs) is of fundamental importance for the majority of their applications. It strongly depends on the type of chemical group used for bonding the molecules forming the SAMs to the selected substrate. Here, we compare the impact of using S and Se bonding groups on the thermal stability of aromatic model SAMs based on naphthalene, containing a polar substituent, and formed on a Au(111) substrate. Using a combination of secondary ion mass spectrometry (SIMS) and X-ray photoelectron spectroscopy (XPS) while heating the samples, we show that the thermal stability of S-bonded SAMs is higher although the bonding between Se and the Au substrate is stronger. This seeming contradiction is found to result from a higher stability of the S–C compared to the Se–C bond. The latter forms the weakest link in the SAMs with Se anchor and, thus, controls its thermal stability. These conclusions are supported by state-of-the art dispersion-corrected density functional theory (DFT) calculations. Notably, full qualitative agreement between the experiments and simulations is obtained only when including Au adatoms in the setup of the unit cells, as these reinforce the bonding between the docking groups and the metal surface. This is an indication for the occurrence of such surface reconstructions also for SAMs consisting of comparably large aromatic molecules.