Carbon in soil affects the formation and stabilization of aggregates (groups of primary particles that adhere to each other more strongly than to surrounding soil particles)1. Soil aggregation is important for preventing soil loss through wind and water erosion, and the size distribution and abundance of water-stable aggregates influences a range of physical, chemical, biological and agricultural properties of soil2. The effects on soil biota and nutrient cycling of increases in soil carbon availability, brought about by increased CO2, are well studied, but the consequences for soil aggregation and structure have not been examined. Here we show for three ecosystems that the water stability and size distribution of aggregates is affected by long-term CO2fumigation, and we propose a mechanism for this that involves the production by fungi of the glycoprotein glomalin.