The responses of threatened tropical avian species to projected climate change and land-use change are important for evaluating the ability of the existing protected areas to provide habitat to these species under future scenarios in biodiversity hotspots. This study uses Maxent, a species distribution model that employs a maximum entropy machine learning approach to map the spatial distributions of habitats suitable for the International Union for Conservation of Nature threatened birds under present and future climate and land-use change in Borneo. We find that the existing protected areas provide very low coverage of the threatened bird species’ suitable habitat areas (95%CI = 9.3–15.4%). Analysis of habitat suitability projections for 18 species of threatened birds suggests that in 2050, under Special Report on Emissions Scenarios A1B and B1, avian species with currently little suitable habitat may gain area but lose in the proportion of this that is protected. Large-ranged species are likely to lose habitat area and this will inflate the proportion of this remaining in protected areas. The present availability of suitable habitat was the most important determinant of future habitat availability under both the scenarios. Threat level, as measured by the International Union for Conservation of Nature and the habitat preferences considered here, Lowland or Lowland–Montane, are poor predictors of the amount of habitat contraction or expansion undergone by the species.