Illegal harvesting negatively affects the forest tree populations, particularly in sub-Saharan Africa, but little is known how fruit production and seedling recruitment are impacted. We assessed recruitment parameters of Balanites aegyptiaca trees in the Dinder Biosphere Reserve (DBR) across 100 sample plots of 25 m x 40 m in both human-impacted (disturbed) and undisturbed sites. We found that the average number of fruiting branches of B. aegyptiaca in the undisturbed sites were three times as high as those in the disturbed sites (F1,98 = 139, P < 0.001). Further, fruiting branches were positively correlated with crown width (R2 = 0.71, beta = 7.1, P = 0.01) across both sites. The height and crown width of B. aegyptiaca in the undisturbed sites were double that of the disturbed sites (F1,196 = 80, P < 0.001; F1,196 = 94.8, P < 0.001). Saplings and seedlings at the undisturbed sites were three times and twice that of the disturbed sites, respectively (F1,196 = 94.5, P < 0.001; F1,196 = 100.8, P < 0.001), with a positive correlation to the average number of fruiting branches (R2 = 0.74, beta = 0.45, P < 0.001). The soil nitrogen and phosphorus contents beneath trees in the undisturbed sites were almost double that of those in the disturbed sites (F1, 196 = 68.1, P < 0.001; F1, 196 = 97.9, P < 0.001) while sodium and electrical conductivity were by about 50% lower (F1, 196 = 535.8, P < 0.001; F1, 196 = 16.1, P < 0.001). We conclude that illegal harvesting in DBR severely reduced tree structure and recruitment parameters of B. aegyptiaca, which might also have impacted soil fertility. We urge for intensive monitoring and awarenessraising programs to conserve this vulnerable tree species.