Strains representing four types of common heat-resistant spores of Bacillus spp., B. cereus CCRC 14655, B. coagulans CCRC10606, B. licheniformis CCRC14693, and B. subtilis CCRC14199, were heated with microwaves at different power levels and under different conditions in salt solutions, starch solutions, and containers. The results of this study showed that B. licheniformis spores had the highest microwave tolerance at a power level of 100% for different incubation times. B. coagulans spores showed the lowest microwave tolerance in salt solutions with water activity values of 0.6, 0.7, 0.8, and 0.9, and B. licheniformis spores were the most resistant in the tested salt solutions at different incubation times. An analysis of the effect of the viscosity of the medium revealed that the bacteria had the lowest microwave resistance in a medium containing <0.8% starch in solution. The microwave resistance levels of the test microorganisms were the lower in glass containers than in polypropylene containers and aluminum foil-enclosed pouches. Of the four species of bacilli, B. licheniformis had the highest microwave tolerance (P < 0.05) under all conditions.