Modifying metal electrodes with self-assembled monolayers (SAMs) has promising applications in organic and molecular electronics. The two key electronic parameters are the modification of the electrode work function because of SAM adsorption and the alignment of the SAM conducting states relative to the metal Fermi level. Through a comprehensive density-functional-theory study on a series of organic thiols self-assembled on Au(111), relationships between the electronic structure of the individual molecules (especially the backbone polarizability and its response to donor/acceptor substitutions) and the properties of the corresponding SAMs are described. The molecular backbone is found to significantly impacts the level alignment; for molecules with small ionization potentials, even Fermi-level pinning is observed. Nevertheless, independent of the backbone, polar head-group substitutions have no effect on the level alignment. For the work-function modification, the larger molecular dipole moments achieved when attaching donor/acceptor substituents to more polarizable backbones are largely compensated by increased depolarization in the SAMs. The main impact of the backbone on the work-function modification thus arises from its influence on the molecular orientation on the surface. This study provides a solid theoretical basis for the fundamental understanding of SAMs and significantly advances the understanding of structure–property relationships needed for the future development of functional organic interfaces.