The interaction between aromatic thiols and the Au(111) surface was investigated using periodic density functional theory (DFT). Different self-assembled monolayers (SAMs) organizations were investigated, namely with different surface reconstructions (flat unreconstructed Au(111) and adatom Au(111) surface). DFT energetics on geometrically optimized SAMs and electronic analysis by means of projected density of states and the crystal orbital Hamilton population method were used to interpret the differences in the adsorption properties. It was found that the adsorption energy difference between the arylthiol chains adsorbed in T-shaped SAMs and adsorbed on flat unreconstructed Au(111) diminishes from long aryl thiols (tpt) to the short ones (dpt and mpt), indicating that the unreconstructed surface becomes more competitive energetically for short-chain arylthiols (dpt and mpt). Moreover, the nature of the Au–S bond was found to be independent of the chain size. This leads us to conclude that the reconstruction, if any, is only dependent on the side-chain interactions.