The aim of this study was to gain information about the effect of thermal treatment of calcium silicate-based sealers. BioRoot RCS (BR), Total Fill BC Sealer (TFBC), and Total Fill BC Sealer HiFlow (TFHF) were exposed to thermal treatment at 37 °C, 47 °C, 57 °C, 67 °C, 77 °C, 87 °C and 97 °C for 30 s. Heat treatment at 97 °C was performed for 60 and 180 s to simulate inappropriate application of warm obturation techniques. Thereafter, specimens were cooled to 37 °C and physical properties (setting time/flow/film thickness according to ISO 6876) were evaluated. Chemical properties (Fourier-transform infrared spectroscopy) were assessed after incubation of the specimens in an incubator at 37 °C and 100% humidity for 8 weeks. Statistical analysis of physical properties was performed using the Kruskal-Wallis-Test (P = 0.05). The setting time, flow, and film thickness of TFBC and TFHF were not relevantly influenced by thermal treatment. Setting time of BR decreased slightly when temperature of heat application increased from 37 °C to 77 °C (P < 0.05). Further heat treatment of BR above 77 °C led to an immediate setting. FT-IR spectroscopy did not reveal any chemical changes for either sealers. Thermal treatment did not lead to any substantial chemical changes at all temperature levels, while physical properties of BR were compromised by heating. TFBC and TFHF can be considered suitable for warm obturation techniques.