Moringa oleifera Lam and Moringa stenopetala (Baker f.) Cufod are being widely promoted as multipurpose trees across the tropics for their nutritional, medicinal and soil health benefits. Different parts of these species are edible, have therapeutic values and their seeds are used for water purification. Although the two species are similar in many ways, they have contrasting distributions. However, their current promotion is not guided by adequate knowledge of the suitability of the target areas. Information is also scanty on the suitability of habitats for these species under the current and future climate change scenarios. Therefore, the objective of this study was to predict the habitat suitability of M. oleifera and M. stenopetala under current and future climate change scenarios using an ensemble of models assuming four shared socio-economic pathways, namely, SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5 for 2050 and 2070. The results suggest that areas that are highly suitable for M. oleifera will increase by 0.1% and 3.2% under SSP1-2.6 to SSP5-8.5 by 2050, respectively. By 2070, the area suitable for M. oleifera would likely decrease by 5.4 and 10.6% under SSP1-2.6 and SSP5-8.5 scenarios, respectively. The habitat that is highly suitable for M. stenopetala was predicted to increase by 85–98% under SSP3-7.0 and SSP5-8.5 scenarios by 2050 and by 2070, while suitable areas could increase by up to 143.6% under SSP5-8.5. The most influential bioclimatic variables for both species were mean diurnal temperature range, mean temperature of driest quarter, precipitation of wettest month, and isothermality. Additionally, soil pH, elevation and water holding capacity were influential variables in the distribution of M. oleifera, while soil pH, soil salinity and slope were influential in M. stenopetala distribution. This study has provided baseline information on the current distribution and possible future habitat suitability, which will be helpful to guide formulation of good policies and practices for promoting Moringa species outside their current range.