Conventional cotton cultivation relies heavily on synthetic inputs, driving environmental degradation, biodiversity loss, serious human health impacts, and widespread pest resistance. Transitioning to organic systems integrating agroecological practices offers a promising pathway toward more sustainable production. This study assessed short-term pest management performance and economic viability of five cotton-based management systems during the first year of conversion in Benin, West Africa: a conventional farmer-practice system and four systems transitioning from conventional to organic production combining sole-cotton cropping or cotton-soybean intercropping, with or without biopesticide applications. Across sites, pest species composition and abundance varied markedly, yet plant injury metrics showed consistent patterns: pesticide use (synthetic or biopesticides) reduced crop damage and increased the proportion of healthy cotton. In central Benin, where bollworm pressure was lower, biopesticide-treated intercrops reduced key bollworms (Earias spp. and endocarpics) but increased the sucking pest Bemisia tabaci, while in northern Benin conventional systems reduced Earias spp. and Diparopsis watersi but slightly increased B. tabaci. Transition-to-organic systems generally supported higher abundances of natural enemies than conventional ones, although diversification effects were site-dependent. Biopesticides did not suppress predator communities, indicating their potential to sustain pest regulation without disrupting ecological functions. Despite lower cotton yields, intercropping improved overall profitability relative to sole-crops in transition to organic and, in several cases, performed similarly to or better than conventional cotton, mainly due to additional soybean production. These findings demonstrate that biopesticide-treated cotton-soybean intercropping can enhance pest regulation and farm profitability during the first year of transition to organic cott