Assessing the future of biodiversity under changing climates is plagued by uncertainty. Drawing on data for sub-Saharan African vertebrates, I focus on some of the major sources of uncertainty surrounding bioclimatic envelope model projections and on possible ways to address them. I examine the uncertainty arising from alternative climate projections and model algorithms and I summarise it through consensus building. To examine ecological uncertainty, I present a framework for teasing apart projected gains, losses, and fragmentation of climatically suitable areas; each of these threats and opportunities can be examined with reference to relevant response-mediating biological traits, such as the species’ climatic tolerance, reproductive output, and dispersal ability. A further source of uncertainty in climate change impact assessments based on bioclimatic envelope models is the omission of narrow-ranging species, which are difficult to model. I demonstrate the conservation implications of such omissions, and I investigate how climate change metrics can be used as an alternative tool in assessments. Multiple metrics of change in climate parameters, seen as proxies for the threats and opportunities facing biodiversity, are reviewed and illustrated at the global scale, and compared to bioclimatic models for sub-Saharan African vertebrates.