Misuse and poor handling of chemical pesticides in agriculture is hazardous to the health of farmers, consumers and the environment. We studied the pest and disease management practices and the type of pesticides used in four root, tuber and banana (RTB) crops in Burundi and Rwanda through in-depth interviews with a total of 811 smallholder farmers. No chemical pesticides were used in banana in either Rwanda and Burundi, whereas the use of insecticides and fungicides in potato is quite frequent. Nearly all insecticides and about one third of the fungicides used are moderately hazardous. Personal protective equipment is used by less than a half of the interviewed farmers in both countries. Reported cases of death due to self- or accidental poisoning among humans and domestic animals in the previous 12 months were substantial in both countries. Training of farmers and agrochemical retailers in safe use of pesticide and handling, and use of integrated pest management approaches to reduce pest and disease damage is recommended.