The study aimed to investigate the relative significance of effects of climatic variability and human disturbance on the population structure of the threatened species Afzelia africana Sm. ex Pers. in the Republic of Benin in West Africa. Forest inventory data such as regeneration density, tree diameter and total height were compiled from A. africana forest stands under different disturbance regimes in the three climatic zones of Benin. Multiple generalised linear models and non-linear diameter–height equations were fitted to contrast the individual effects of categorical variables, such as climatic zone and disturbance level. Results revealed significantly higher scaling coefficients in less drier regions and low-disturbance stands. The diameter–height relationship was more controlled by the climatic zone than by the disturbance level. Accordingly, the disturbance level contributed only to the intercept of the diameter–height model, whereas the climatic zone significantly influenced both intercept and slope. In addition, when climatic zone and disturbance level were considered as sources of variation in the diameter–height model, the former explained the greater marginal variance. It was concluded that climate has the greater effect on population structure of A. africana in natural stands.