Gender differentials in agricultural productivity are likely to vary considerably between different agroecological zones. A thorough understanding of the location and causes of gender disparities are needed in order to formulate effective policies for addressing the gap. Exemplified on Cameroonian smallholder plot-level data, we examine the determinants of gender disparities in productivity separately for three agroecological regions e.g., Sahel, Western Highlands, and Bimodal Rainfall Humid Forest. We account for selectivity bias, employ an extended Oaxaca-Blinder decomposition, and a distributional decomposition using percentile weighted regressions. We found that gender disparities differ across agroecological zones and gender indicators: they are more acute in the arid Sahel for almost all plot headships, followed by the Western Highlands, while productivity is biased toward all women in the Bimodal Rainfall Humid Forest. We also found that gender disparities are the result of unobserved factors in all regions and plot headships. Women’s structural disadvantage drives gender differences in returns to inputs with contributing factors differing by gender indicator and region. In all regions and plots, the endowment effect is larger for the poorest and wealthiest farmers and its drivers are neither gender-neutral nor the same in all agroecological areas. Gender and regional differences in the results suggest that policies should be gender and region-specific.