Differences in heating of silicon and silicon-on-insulator (SOI) substrates in molecular beam epitaxy were revealed by low-coherence tandem interferometry. Using this technique the interference effects which impede the correct evaluation of SOI substrate temperature by infrared pyrometers can be eliminated and so the reliable temperature readout can be achieved. It was shown that at the same thermocouple and heater power settings the real temperature of SOI substrates is higher than of silicon ones and the difference may be as high as 40-50 degrees C at temperatures close to 600 degrees C. It is supposed that such effect is caused by the additional absorption of heater radiation by the buried oxide layer in the mid-infrared range. Independent proof of this effect was obtained by growing on both types of substrates a series of structures with self-assembled Ge nanoislands whose parameters are known to be very temperature sensitive. The proposed low-coherence interferometry technique provides precise real-time control of the growth temperature and so allows formation of SiGe nanostructures with desired parameters. (C) 2016 Elsevier B.V. All rights reserved.