The negative effects of pest infestation on agricultural production cannot be underestimated. There have been several efforts to control these pests, chiefly through the use of synthetic pesticides. However, the continuous use of the chemicals causes pest resistance and resurgence and presents high human and environmental risks. This study examines the economic, health, and environmental impacts of Tuta absoluta (Meyrick 1917), an economically important pest in tomato production, among smallholder farmers in selected counties in Kenya and Uganda. Economic Impact Quotient and gross margin analysis were used on data obtained from a random sample of 316 and 345 tomato growers in Kenya and Uganda, respectively.The results show a significant impact of T. absoluta on tomato production in both countries. On average, the tomato growers earned a gross income of $38,123 and $11,627 in Kenya and Uganda, respectively, with synthetic chemicals for the management of T. absoluta contributing 66–78% of the cost of production. The opportunity cost lost due to forgoing pesticide for management of the pest, and instead replacing it with an integrated pest management package was valued between $8 and $646 in Kenya and $895 in Uganda, respectively, using net present value through the most pessimistic scenario, while benefit–cost ratio was $1 and $5 in Kenya and Uganda, respectively.