Abstract In this paper, the tuning of the thermopower with single-molecule junctions of fullerene (C60), 4,4?-bipyridine (BPY), and p-phenylenediamine (PPD) using scanning tunneling microscopy (STM)-based break junction technique is demonstrated. Single-molecule junctions are prepared in a nanogap between a Au-STM tip and a Au(111) electrode. Upon applying a temperature difference across the junction, a thermoelectric voltage is generated across it. By mechanically controlling the tip?electrode separation distance, the thermoelectric voltage of the junction is tuned. The absolute value of the thermopower decreases with decreasing tip?electrode separation distance for BPY and PPD, while it increases for C60. Atomistic simulations of the junction illustrate how this arises from shifts in the conduction orbital energies induced by the mechanical compression of the junctions.