Livestock browsing, and illegal harvesting often influence natural woodlands, rangelands, and biosphere reserves. However, the resulting tree species diversity, composition, and population structure have rarely been quantified. This study explored the status of tree diversity, composition, and the growth of Balanites aegyptiaca, across 100 sample plots of 25 m x 40 m at disturbed and non-disturbed sites in Dinder Biosphere Reserve, Sudan (DBR). The dendrometric parameters of B. aegyptiaca, fruit production, and the soil-chemical properties were also assessed in the same sample plots. Moreover, to examine the response of B. aegyptiaca seedlings and saplings to livestock browsing, the study used a stratified sampling design with four sites been browsed by goats, cattle, camels, and control, respectively. The study data was collected over two years from January 2019 to January 2021. It was observed that non-disturbed sites had double tree diversity than that of disturbed ones (T = 32.6, p < 0.001), and their seedlings and saplings constituted more than 70% of the entire population (F2,48 = 116.4, p = 0.034; F2,48 = 163.2, p = 0.021, respectively). The soil nitrogen and phosphorus contents beneath trees in non disturbed sites were almost double that of those in the disturbed site (F1, 196 = 68.1, p < 0.001; F1, 196 = 97.9, p < 0.001, respectively) while sodium and electrical conductivity were by about 50% lower (F1, 196 = 535.8, p < 0.001; F1, 196 = 16.1, p < 0.001, respectively). Mortalities of seedlings under goat browsing were four times higher than that under camel browsing and control and twice as high than under cattle browsing (F3,196 = 100.39, p < 0.001). Sapling mortality was three times higher under goat browsing compared to cattle and control (F3,196 = 73.4, p < 0.001). The study found that seedlings recover better than saplings, and, unexpectedly, goat browsing severely affected the natural regeneration of B. aegyptiaca in DBR. Illegal harvesting in DBR severely reduced tree structure and recruitment parameters of B. aegyptiaca, which might also impact soil fertility. Intensive monitoring and awareness-raising programs are urgently needed to conserve this vulnerable tree species.