Common bean production is constrained by a multitude of biotic constraints including bean flies and Fusarium wilt in tropical and subtropical farming systems globally. As these pests and diseases attack the crop beneath the soil, excessive applications of synthetic pesticides are frequently used for their control. The use of plant-based pesticides could be a more sustainable management approach; however, few studies have investigated their application for controlling soil-borne pests and diseases. This study aimed to evaluate the efficacy of pesticidal plants and soil fertility management for controlling bean fly (Ophiomyia spp.) and Fusarium wilt (Fusarium spp.) using extracts and pastes of Azadirachta indica, Tephrosia vogelii, Tagetes minuta, Lippia javanica, Cymbopogon citratus and Ocimum gratissimum. To protect against Fusarium wilt and bean fly, pesticidal plants were applied as a seed coating and/or foliar spray, and demonstrated that common bean seeds coated with T. vogelii resulted in higher yields than other pesticidal plants and the synthetic pesticide control treatment. Treatments to target bean fly damage showed no significant difference between application methods on the oviposition rate of bean fly. An integrated treatment of T. minuta with 2 g Diammonium phosphate fertilizer and high compost led to higher yields than other treatments. Our results indicate that key soil-borne pests and pathogens of common bean can be effectively managed without synthetic pesticide inputs, while seed ball pastes of pesticidal plants combined with soil fertility management can increase crop yields using cost-beneficial agroecological farming systems.