Photoautotrophic surface communities forming biological soil crusts (biocrusts) are crucial for soil stability as well as water, nutrient and trace gas cycling at regional and global scales. Quantitative information on their global coverage and the environmental factors driving their distribution patterns, however, are not readily available. We use observations and environmental modelling to estimate the global distribution of biocrusts and their response to global change using future projected scenarios. We find that biocrusts currently covering approximately 12% of Earth’s terrestrial surface will decrease by about 25–40% within 65 years due to anthropogenically caused climate change and land-use intensification, responding far more drastically than vascular plants. Our results illustrate that current biocrust occurrence is mainly driven by a combination of precipitation, temperature and land management, and future changes are expected to be affected by land-use and climate change in similar proportion. The predicted loss of biocrusts may substantially reduce the microbial contribution to nitrogen cycling and enhance the emissions of soil dust, which affects the functioning of ecosystems as well as human health and should be considered in the modelling, mitigation and management of global change.