In South African savanna and grassland, exclusion of ecological disturbances (fire, herbivory) led to increases in woody cover. Resultant changes in edaphic properties (Mg, pH, Ca) drove bacterial community structure while changes in vegetation drove fungal community structure. Despite differences between fire and herbivory treatments, there was relatively little impact on soil microbial communities, soil organic carbon and other soil characteristics. We conclude that soil microbial communities in disturbance-driven grassy biomes are resistant to change.