No information exists on the susceptibility of arbuscular mycorrhizal fungal (AMF) communities in Canadian prairie agriculture soils to climate change. An experiment was initiated in mid-May 2011 in which replicated soil cores were transplanted reciprocally from four cultivated prairie sites in Saskatchewan, Canada, representing different regional climatic zones ranging from semiarid to subhumid regional climates, such that replicated (n = 4) soil cores from each site were present at all sites. Field pea was grown in all cores and at harvest in early-September 2011; soil samples were collected to analyze the changes of AMF communities over the cropping season. A total of 82 operational taxonomic units belonging to eight AMF genera were identified using 18S rRNA gene pyrosequencing. When soils were transplanted to new environments, the relative abundance of AMF changed considerably. Typically, Shannon diversity declined when soil cores were transplanted to new environments. We present evidence that with the altered climatic conditions following transplantation of soil cores, the relative abundance of AMF was significantly altered, and some taxa were enhanced, suppressed, or disappeared in the home-away soils compared with home-site soils. This study implies that the future climate change effects on AMF may impact specific phylogenetic taxa differently, such that rare species or those with low abundance may increase or decrease with unknown consequences. Understanding the potential responses of AMF communities to soil–climate interactions is important when considering the impacts of climate change on soil microbial communities.