FLP-catalyzed hydrogenations of 15 substrates were compared using microwave irradiation and conventional heating. The direct comparison revealed that a rate acceleration of up to 2.5 was achieved in the presence of microwaves. This heating method is particularly promising for the hydrogenation of nitrogen-containing heterocycles. Acridine, quinines and especially 1-methyl indole were reduced very efficiently under mild conditions and only 4 bar hydrogen pressure in high yields.