This article examines pest management practices recommended to smallholder farmers by extension agents, and the factors influencing the same. The study focused on plant health clinics, established under the Plantwise program, as primary providers of data. A diverse range of biotic and abiotic stressors was found to hamper crop production in the smallholder agricultural subsector of Kenya. Much as extension workers prescribed Integrated Pest Management (IPM) practices, albeit on a limited scale, management of crop pests was mainly by use of non-IPM practices. In addition, significant associations were observed between the prescribed practice and individual moderators (namely extension officer’s gender, age, education level, and location), type of crop and causative agent. The results of the study confirm the need for further investments in the smallholder agricultural subsector of Kenya. In particular, the sector should prioritize capacity-building initiatives for extension agents on ecological and economical sound approaches to pest management.