Molecular junctions are a versatile test bed for investigating nanoscale thermoelectricity1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and contribute to the design of new cost-effective environmentally friendly organic thermoelectric materials11. It was suggested that transport resonances associated with discrete molecular levels could play a key role in thermoelectric performance12, 13, but no direct experimental evidence has been reported. Here we study single-molecule junctions of the endohedral fullerene Sc3N@C80 connected to gold electrodes using a scanning tunnelling microscope. We find that the magnitude and sign of the thermopower depend strongly on the orientation of the molecule and on applied pressure. Our calculations show that Sc3N inside the fullerene cage creates a sharp resonance near the Fermi level, whose energetic location, and hence the thermopower, can be tuned by applying pressure. These results reveal that Sc3N@C80 is a bi-thermoelectric material, exhibiting both positive and negative thermopower, and provide an unambiguous demonstration of the importance of transport resonances in molecular junctions.