The soil microbiome is responsible for mediating key ecological processes, however little is known about its sensitivity to climate change. Observed increases in atmospheric [CO2] and alteration to rainfall patterns, due to anthropogenic release of greenhouse gases, will likely have a strong influence on soil microbial communities and ultimately the ecosystem services they provide. Therefore, it is vital to understand how soil microbial communities will respond to future climate change scenarios. In a large climate change experiment, we surveyed soil fungal community structure changes under Eucalyptus saligna exposed to a 3-year period of elevated [CO2] and one year of drought. Our results suggest that drought is a key factor in shaping soil fungal community composition and its interactive effect with elevated [CO2] appears to select for a fungal community that is more adapted to drought conditions. In-depth examination of fungal community composition showed that plant pathogenic strains, such as Fusarium sp. and Mycosphaerella sp., appear to be well adapted to climate change conditions, which may have significant implications for eucalypt plantation forest health under future climate conditions. Overall our results indicate that soil water availability regulates the abundance and diversity of the soil fungal community.