Weed management is a key to the adoption of conservation agriculture practices in Sub-Saharan Africa. This study assessed the effect of conservation agriculture practices, strip-tillage and direct mulch-based cropping system on weed emergence, biomass and community structure in cotton-based cropping systems in northern Benin. The experiment was conducted in 2023 and 2024 using a randomized complete block design with three replications under three cropping systems: conventional tillage, strip tillage (cotton in biannual rotation with maize-cowpea intercropping over strip tillage) and direct mulch-based cropping system (cotton in three-season rotation with maize and Stylosanthes guianensis intercropping and sorghum and soybean intercropping over direct mulch-based cropping system). Weed emergence and species were inventoried at seven-day intervals starting from the first rainfall triggering their germination. Weed biomass was measured at each weeding. Conservation agriculture systems significantly reduced weed emergence compared to conventional tillage. The reductions were 15¿% (cotton) and 46¿% (maize) under strip tillage, and 33¿% (cotton) and 56¿% (maize) under direct mulch-based cropping system. Weed biomass increased significantly under the strip tillage system, i.e. by 40¿% in cotton plots and by 41¿% in maize plots. Crop yields were not significantly affected by systems. Weed community structure was shaped by the interaction between the cropping system and seasons, with distinct indicator species associated with cropping systems. These findings demonstrate that conservation agriculture practices can reduce weed emergence and alter weed community structure without compromising yield performance. This is the first study to characterize weed management under conservation agriculture in Sub-Saharan African cotton-based cropping systems.