The self-assembly of the naphthylmethylamine molecules (NMA) on the Au(111) surface is investigated by a combined experimental and theoretical approach. Three well-defined phases are observed upon different thermal treatments at the monolayer stage. The role played by the methylamine termination is evidenced in both the molecule–molecule and molecule–substrate interactions. The autorecognition process of the amino groups is identified as the driving factor for the formation of a complex hydrogen bonding scheme in small molecular clusters, possibly acting also as a precursor of a denitrogenation condensation process induced by thermal annealing.