Two independent techniques, one intrusive and one non-intrusive, for monitoring the thermal performance of in situ roof systems are compared. The intrusive technique requires thermocouples on inside and outside surfaces of the roof system and a heat flux transducer (HFT) embedded in the system. The non-intrusive procedure has the same thermocouple placement and a series of HFTs on the inside surface of the deck. The crucial difference in the methods is in the HFT placement and the technique for HFT calibration. Results of a one-year field study using both methods on the same roof assembly are described. The roof assembly is a built-up roof with molded expanded polystyrene (EPS) insulation above a metal deck.