Bacillus endospores can survive milk pasteurization, and later germinate and grow during further processing of milk. Their resistance to various physical and biochemical treatments, dormancy, ability to adhere to the surfaces of process equipment resulting in biofilm formation, and prompt germination under favorable conditions, make them important contaminants in dairy processes. The objective of this research was to investigate the effect of hydrodynamic cavitation in a continuous mode, and its combination with thermal treatment, to reduce Bacillus spores in milk. We hypothesized that cavitation would induce germination of spores and any post cavitation heat treatment would lead to their inactivation. Spores of Bacillus licheniformis (ATCC 6634) were produced in lab by incubating on brain-heart infusion (BHI) agar plates for about 2 weeks, and were harvested from plates by washing and centrifugation. The vegetative cells in spore suspension were inactivated by heating at 85°C for 10 min. The resulting spores were inoculated in sterile skim milk to a level of log 2 cfu/mL. Inoculated milk samples at 10°C were passed through APV Cavitator (SPX, Denmark) at 60 Hz frequency using 4-row rotor in 6-mm housing. The exposure time of 22 s per pass was provided at 200 L/h flow rate with a back pressure of 120 kPa. The milk containing endospores was recirculated for 25 min (a total exposure time of 183 s) with a temperature rise to 99°C. Samples were cooled and held for 3 h at 30°C to let the germination process occur. Samples were then heated at 85°C for 15 min, and were plated on BHI agar medium. Experiments were conducted as replicates of 2, and were repeated thrice. Statistical significance of the data at P < 0.05 was determined using the SAS software. A significant difference was observed in the endospore counts after the treatments. Heat treatment alone did not result in inactivation of the spores. Whereas, cavitation with holding followed by heat treatment caused a reduction with only 0.60 log survivors. In conclusion, it was evident that a combined process with cavitation effect, holding for germination, followed by thermal treatment can be effectively used to inactivate thermoduric endospores.