Climate change is predicted to disproportionately impact sub‐Saharan Africa, with potential devastating consequences on plant populations. Climate change may, however, impact intraspecific taxa differently. The aim of the study was to determine the current distribution and impact of climate change on three varieties of Vachellia sieberiana, that is, var. sieberiana, var. villosa and var. woodii. Ensemble species distribution models (SDMs) were built in “biomod2” using 66, 45, and 137 occurrence records for var. sieberiana, var. villosa, and var. woodii, respectively. The ensemble SDMs were projected to 2041–2060 and 2081–2100 under three general circulation models (GCMs) and two shared socioeconomic pathways (SSPs). The three GCMs were the Canadian Earth System Model version 5, the Institut Pierre‐Simon Laplace Climate Model version 6A Low Resolution, and the Model for Interdisciplinary Research on Climate version 6. The suitable habitat of var. sieberiana predominantly occurs in the Sudanian and Zambezian phytochoria while that of var. villosa largely occurs in the Sudanian phytochorion. The suitable habitat of var. woodii mainly occurs in the Zambezian phyotochorion. There is coexistence of var. villosa and var. sieberiana in the Sudanian phytochorion while var. sieberiana and var. woodii coexist in the Zambezian phytochorion. Under SSP2‐4.5 in 2041–2060 and averaged across the three GCMs, the suitable habitat expanded by 33.8% and 119.7% for var. sieberiana and var. villosa, respectively. In contrast, the suitable habitat of var. woodii contracted by −8.4%. Similar trends were observed in 2041–2060 under SSP5‐8.5 [var. sieberiana (38.6%), var. villosa (139.0%), and var. woodii (−10.4%)], in 2081–2100 under SSP2‐4.5 [var. sieberiana (4.6%), var. villosa (153.4%), and var. woodii (−14.4%)], and in 2081–2100 under SSP5‐8.5 [var. sieberiana (49.3%), var. villosa (233.4%), and var. woodii (−30.7%)]. Different responses to climate change call for unique management and conservation decisions for the varieties.