While soil biota and processes are becoming increasingly appreciated as important parameters for consideration in global change studies, the fundamental characteristic of soil structure is a neglected area of research. In a sorghum [Sorghum bicolor (L.) Moench] field experiment in which CO2[supplied using free-air CO2 enrichment (FACE) technology] was crossed factorially with an irrigation treatment, soil aggregate (1–2 mm) water stability increased in response to elevated CO2. Aggregate water stability was increased by 40% and 20% in response to CO2, at ample and limited water supply treatments, respectively. Soil hyphal lengths of arbuscular mycorrhizal fungi (AMF) increased strongly (with a threefold increase in the dry treatment) in response to CO2, and the concentrations of one fraction (easily extractable glomalin, EEG) of the AMF-produced protein glomalin were also increased. Two fractions of glomalin, and AMF hyphal lengths were all positively correlated with soil aggregate water stability. The present results further support the hypothesis that AMF can become important in global change scenarios. Although in this field study a causal relationship between hyphal length, glomalin and aggregate stability cannot be demonstrated, the present data do suggest that AMF could mediate changes in soil structure under elevated CO2. This could be of great importance in agricultural systems threatened by erosional soil loss.