We measured the Seebeck coefficient for junctions comprising self-assembled monolayers and bilayers of the fullerene moiety PTEG-1 on Au using eutectic Ga–In in a controlled anhydrous atmosphere by varying the temperature gradient from −12 to 12 °C, observing a linear response in thermovoltage across the range. The sign of the coefficient was positive for monolayers of PTEG-1, (195 ± 8) μV K–1 and negative for bilayers of PTEG-1, (−209 ± 14) μV K–1, indicating a change from HOMO-mediated to LUMO-mediated charge-transport. Charge-transport is nonresonant tunneling for both monolayers and bilayers, but the former self-assembles with the fullerene cage at the chemisorbed interface while the latter includes a fullerene cage at the physisorbed interface, demonstrating that the physical position of the fullerene cage determines the energetic position of the frontier molecular orbitals of PTEG-1.