Postharvest management of grain and seed is a challenge among smallholder farmers. Limited information is available on how smallholder farmers in eastern Democratic Republic of Congo (DRC), who have been exposed to multiple conflicts, manage grain and seed after harvest. We interviewed 690 smallholder farmers in Lubero (Baswagha chiefdom) and Rutshuru (Bwisha and Bwito chiefdoms) territories of the North Kivu province of the DRC to assess how they dried and stored their crops. Results reveal that 95% and 80% farmers produced beans and maize, respectively. About half of respondents in Bwisha grew soybean, suggesting production diversification using conflict-resistant crops to minimize thefts and looting. Rotting and theft were the major challenges during field drying, while insects (81.3%) were the most important issue during storage. Sixty-six percent of farmers did not protect their grain during storage, exposing it to insect damage. Farmers producing beans in both Bwisha and Bwito, farmers storing beans and maize, and those storing for more than three months were more likely to protect their grains during storage. More than 70% of farmers saved seed for planting the next season but suffered significant weight losses of up to 50% due to insects. Storing grain in hermetic bags for six months had an estimated return on investments of up to 63% for maize in Baswagha and 54% for beans in Bwisha. Improved drying and storage technologies would help smallholder farmers to reduce their grain postharvest losses due to mold, theft, and insects. Smallholder farmers using these improved postharvest technologies have the opportunity to secure quality grain for home consumption and sale, and seed for planting.