Buckwheat (Fagopyrum esculentum, Moench) is a specialty crop of interest because of its numerous nutritional, health, and agronomic benefits. A high microbial load on the seed often limits its export and use in functional foods; therefore, these generally recognized as safe antimicrobial treatments were evaluated for buckwheat disinfection: ozone gas, ozonated water, acetic acid (AA), acidic calcium sulfate (ACS), and combinations thereof. The liquid treatments were sprayed on buckwheat grain in a fluidized bed and the treated buckwheat was analyzed for aerobic plate count (APC) and yeast and mold count (YMC). Ozone gas and ozonated water treatments were not significantly (P < 0.05) effective in reducing the microbial load, and AA + ozonated water had significant but low effectiveness. Electron microscopic imaging suggested that rough surfaces and crevices in the seed hull shielded microbes from ozone treatments. Effectiveness of treatments was also limited by the industry limits on the amount of moisture that can be added to buckwheat grain. The ACS (50 mL/L) treatment was most effective with 3.9-log10 reduction in APC and complete elimination of YMC. ACS (50 mL/L) caused bleaching and increased redness. Sufficient reduction of microbes could be achieved at a lower concentration of ACS, thereby reducing the effect on color.