Small-scale interventions on training medicine retailers on malaria treatment improve over-the-counter medicine use, but there is little evidence on effectiveness when scaled up. This study evaluated the impact of Ministry of Health (MoH) training programs on the knowledge and practices of medicine retailers in three districts in Kenya. A cluster randomized trial was planned across 10 administrative divisions. Findings indicated that 30.7% (95% confidence interval [CI]: 23.3, 39.0) and 5.2% (95% CI: 2.1, 10.3) of program and control retailers, respectively, sold MoH amodiaquine with correct advice on use to surrogate clients (OR = 8.8; 95% CI: 2.9, 26.9; P < 0.001). Similarly, 61.8% (95% CI: 54.2, 69.1) and 6.3% (95% CI: 2.7, 12.1) of program and control retailers, respectively, reported correct knowledge on dosing with amodiaquine (OR = 29.8; 95% CI: 8.2, 108.8). Large-scale retailer training programs within the national malaria control framework led to significant improvements in retailers' practices across three districts.