Understanding how multiple disturbances affect species population structure is crucial for designing a better conservation strategy of threatened species. In this paper, we assessed the disturbance patterns and evaluated their effects on the population structure of Afzelia africana, in two different bioclimatic zones of the Republic of Benin. The main disturbances in the studied area included branch pruning and debarking. Individuals of medium size (20-40 cm) were mostly pruned and debarked. The percentages of pruning and debarking were similar at population level across the two studied bioclimatic zones (t = −0.04, p = 0.96; t = 0.73, p = 0.48). Examining this at individual level, pruning was similar but debarking was higher in the Sudanian zone (12.14 ± 0.93%) than in the Sudano-Guinean zone (7.44 ± 0.88) (W = 40859, p < 0.001). Population structure was bell-shaped in the Sudanian zone regardless of the disturbance level. In contrast, in the Sudano-Guinean zone, mildly disturbed populations showed an inverse J-shaped structure, whereas those highly disturbed were bell-shaped. This underlined the climatic (dryness) and disturbance effects on the establishment and recruitment of small trees into the next life stage in tropical savanna ecosystems. Good regeneration pattern and the largest individuals were found within the protected areas, demonstrating the prominent role of protected areas for the species conservation. Therefore, we suggested that conservation efforts should be extended to populations outside the protected areas. Forestry department should establish firebreaks networks to protect small individuals and facilitate their recruitment, as well as the regulation and enforcement should be improved on the sustainable use of the species.