Abstract In this paper, we investigated the heat transfer and temperature measurement during thermodiffusion experiments using the Selectable Optical Diagnostics Instrument (SODI) apparatus at reduced gravity. The principles of Mach Zehnder Interferometry (MZI) were used for the measurement of various parameters, such as temperature and concentration, in transparent cells in the SODI apparatus on board the International Space Station (ISS). In particular, the critical behavior of heat flux at the cell boundaries was studied. We discuss deviations between the temperature differences at the hot and cold sides of the cell when measured using optical image processing and Peltier elements, and we suggest a reason for this discrepancy. According to the extent of this experimental method, we provide the necessary adjustments to have accurate post-processing for MZI thermodiffusion experiments. The quality and accuracy of the thermal controller unit of the SODI apparatus were also studied. The sensitivity of the temperature measurements using interferometry was carried out, and we found good performance of this method in a microgravity environment. The effects both of the weak insulation at the walls and of the separation distance between the hot and cold sides of the cell are discussed. While the thermal unit of the SODI apparatus controlled the temperature across the cell within an acceptable accuracy range for all of the thermodiffusion experiments, marginal differences between various SODI experiments were observed and reported in this study. Finally, we discuss the impacts of different measurement techniques for the temperatures in the thermodiffusion experiment. Comparing the results of this study with literature shows that the enhancement of heat transfer analysis can lead to a more accurate measurement of the Soret coefficient.