Habitat transformation and loss is one of the greatest threats currently facing avian species. The cumulative impact of climate change on habitat loss is projected to produce disproportionate risk for endemic high-altitude species. The Southern Bald Ibis (Geronticus calvus) is an endemic high-altitude species found throughout highland grassland habitats in South Africa and Lesotho. The historical distribution has contracted notably and causal factors remain ambiguous. Furthermore, the historical population (1950–1970) was believed to be stable, but recent local surveys suggest colony declines and the current global population status remains largely unquantified. We assessed the current distribution and population status of the species through predictive modeling and trends in historical and recent colony counts across the species’ range. We examined climate and habitat change as potential causal factors contributing to the historical contraction in distribution, and projected the potential impact of future climate change predicted by global circulation models. Our study confirms that Southern Bald Ibis are of conservation concern. The loss of grasslands to expanding woody vegetation through bush encroachment was the most detrimental habitat transformation type associated with decreased colony growth and colony collapse. We recommend maintaining a minimum threshold of 50% or greater intact grassland habitat surrounding colonies to reduce colony extinction risk and promote colony persistence.