Burkina Faso, a West Africa's country, primarily relies on agriculture to drive its economic growth. However, in the country, this sector has not been consistently developed to deal with climate risks and market failures. Even though the cotton sector in Burkina Faso is well structured in a value chain, producers achieve low factor productivity. Given the complexity of cotton production, its high sensitivity to climate, and the uncertain and erratic weather conditions, it is relevant to analyze the heterogeneous effects of climate variability on farmers' productive performance. The study investigated this issue by estimating a mixed production translog function applied to Burkina Faso farmers' data using the feasible generalized least squares estimator and control function approach, and controlling for socioeconomic factors. The findings demonstrate that weather and climate fluctuations are the adverse effects on cotton output, contingent upon individual farmer characteristics and the specific agroclimatic context of production. These results underscore the heterogeneous nature of climate change effects, providing confirmation that the effects of rainfall, temperature, and wind variability are non-uniform and more crucial for agricultural activities in some regions. In this regard, strategic and localized agricultural policies emerge as indispensable tools for bolstering the resilience of agricultural systems in the face of shifting climatic paradigms. Thereby, the study recommends the need for water- and heat-stress-resilient crop varieties and region-specific climate-smart agricultural technologies at scale, including irrigation and sustainable innovation programs.