One of the fundamental questions in soil microbial ecology is whether or not the diversity and structure of microbial communities influence the functioning of terrestrial ecosystems. We used a semi-arid, soil chronosequence within the San Francisco Volcanic Field in northern Arizona to evaluate if soil nutrient cycling processes covaried with the diversity and structure of resident soil microbial communities. As has been found previously in soil chronosequences in more humid ecosystems, soil phosphorus availability was greatest in younger soils and decreased over the three million year substrate-age gradient. Also similar to more humid ecosystems, nitrogen availability increased with soil development, but declined at the oldest site. Additionally, within each site, the relative availabilities of these nutrients varied strongly with canopy type (under Juniperus monosperma or Pinus edulis canopies or within intercanopy spaces). We characterized major soil microbial groups among these contrasting sites and canopy types using phospholipid fatty acids, while community diversity and structure of ectomycorrhizal fungi and chemolithotrophic nitrifiers were assessed using molecular techniques. Our results suggest that microbial communities associated with different degrees of soil development and contrasting canopy types may substantially alter rates and patterns of nutrient cycling during ecosystem development. Although these and previous correlative approaches toward evaluating the importance of soil microbial structure to ecosystem function are suggestive, more studies that experimentally manipulate nutrient cycling rates across broad ecosystem gradients are needed to unequivocally link the importance of identity and arrangement of soil microorganisms to the function of terrestrial ecosystems.