Aflatoxin contaminated maize is of public health concern in Kenya. Training farmers on good agricultural practice (GAP) has been touted as a mitigative measure. Little is known of the effect of such training on aflatoxin levels in maize grown in Kenya. This study evaluated what effect training farmers on GAP has on aflatoxin levels in maize grown in Kaptumo, Kilibwoni, and Kipkaren divisions in Nandi County, Kenya. Ninety farmers were recruited into farmer field schools and a questionnaire on GAP administered to each farmer. Maize samples were collected from the farmers and analyzed for aflatoxins using competitive enzyme-linked immunosorbent assay (c-ELISA). All farmers weeded their farms before planting, prepared the land, correctly spaced the seedlings, sorted the maize after shelling, cleaned stores before use and knew that aflatoxins were harmful to humans and animals. Eighty-one farmers did early planting, 88/90 did stooking after harvesting, 89/90 applied fertilizer, 89/90 cleared bushes around the stores, 87/90 used wooden pallets to store maize, 89/90 dried maize after harvesting, 83/90 did crop rotation, and 89/90 used clean transport. Moreover, 62/90 had a relative who had died from liver cancer, 13/90 had fed damaged/rotten seeds to animals, and 45/90 had stored harvested seeds on the ground. The mean aflatoxin levels in season 1 were significantly different from season 2 (1.918 ± 1.065; 1.301 ± 1.501). Our findings suggest that some aspects of the training on GAP were better received than others. Training farmers on GAP results in a decrease in aflatoxin levels in maize grown in Nandi County. Farmers in other maize growing areas of Kenya may benefit from similar training on GAP.