Alfalfa seeds were inoculated with a three-strain cocktail of Escherichia coli O157:H7, Salmonella enterica subsp. enterica serovar Typhimurium DT104, or Listeria monocytogenes by immersion to contain ∼6 to 8 log CFU/g and then treated with a fatty acid–based sanitizer containing 250 ppm of peroxyacid, 1,000 ppm of caprylic and capric acids (Emery 658), 1,000 ppm of lactic acid, and 500 ppm of glycerol monolaurate at a reference concentration of 1×. Inoculated seeds were immersed at sanitizer concentrations of 5×, 10×, and 15× for 1, 3, 5, and 10 min and then assessed for pathogen survivors by direct plating. The lowest concentration that decreased all three pathogens by >5 log was 15×. After a 3-min exposure to the 15× concentration, populations of E. coli O157:H7, Salmonella Typhimurium DT104, and L. monocytogenes decreased by >5.45, >5.62, and >6.92 log, respectively, with no sublethal injury and no significant loss in seed germination rate or final sprout yield. The components of this 15× concentration (treatment A) were assessed independently and in various combinations to optimize antimicrobial activity. With inoculated seeds, treatment C (15,000 ppm of Emery 658, 15,000 ppm of lactic acid, and 7,500 ppm of glycerol monolaurate) decreased Salmonella Typhimurium, E. coli O157:H7, and L. monocytogenes by 6.23 and 5.57 log, 4.77 and 6.29 log, and 3.86 and 4.21 log after 3 and 5 min of exposure, respectively. Treatment D (15,000 ppm of Emery 658 and 15,000 ppm of lactic acid) reduced Salmonella Typhimurium by >6.90 log regardless of exposure time and E. coli O157:H7 and L. monocytogenes by 4.60 and >5.18 log and 3.55 and 3.14 log after 3 and 5 min, respectively. No significant differences (P > 0.05) were found between treatments A, C, and D. Overall, treatment D, which contained Emery 658 and lactic acid as active ingredients, reduced E. coli O157:H7, Salmonella Typhimurium, and L. monocytogenes populations by 3.55 to >6.90 log and may provide a viable alternative to the recommended 20,000 ppm of chlorine for sanitizing alfalfa seeds.