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Development of soil microbial communities is driven by local abiotic and biotic conditions, yet our current understanding of their ecology is limited to studies in modified or young and relatively fertile ecosystems. In nutrient-impoverished soils, microbial communities may be predominantly structured by availability of key elements such as phosphorus (P) or nitrogen, regardless of the taxa (bacteria, archaea or fungi). Here, we determined if shifts in bacterial communities and biomass occurred along a long-term soil chronosequence in south-western Australia, and whether such shifts were related to changes in soil nutrient availability along the retrogressive phase of this chronosequence. We quantified shifts in the biomass and abundance of major soil microbial groups using phospholipid fatty acids and quantitative polymerase chain reaction. We found that declining soil P availability limited microbial growth and community structure. Common cations, notably magnesium, showed strong relationships with the abundance of most bacterial and archaeal taxa. In the oldest most severely impoverished soils, the fungal to bacteria ratio was higher than in the young soils, indicating fungi are better adapted to such environments. Finally, archaeal copy numbers decreased more strongly than bacterial copy numbers with increasing nutrient-impoverishment of soils. The study enhances our understanding of the ecology of soil bacteria, archaea, and fungi during ecosystem development and retrogression. • Declining soil phosphorus (P) availability appeared to limit microbial growth and abundance. • Common cations, particularly magnesium, appeared important for the abundance of most bacterial and archaeal taxa. • Our data suggest that fungi are likely better adapted to severely nutrient-impoverished soils than bacteria are. [ABSTRACT FROM AUTHOR]