We present a scanning tunneling microscopy study of decanethiol on Au(001) in the low coverage regime. As expected, the hex reconstruction is lifted, however, no ordered decanethiol phases form. We observe large areas free of Au islands and covered with a disordered decanethiol phase. I(t) spectroscopy measurements suggest that this disordered phase is dynamic and most likely comprises diffusing Au adatoms, decanethiol molecules, and/or Au-adatom-decanethiol molecule complexes. We have performed density functional theory calculations and show that the activation barrier for diffusion is lower when Au-adatom-molecule complexes are considered in comparison to the case of bare molecule. These findings suggest that although no vacancy pits form on Au(001), Au-adatoms expelled during the lifting of the hex reconstruction may be still important for the diffusion of thiol molecules on this surface.