Microbial communities are responsible for biogeochemical processes in soils such as nutrient cycling and organic matter formation, which are essential to the establishment of vegetation and ecosystem sustainability. Phospholipid fatty acid analysis, microbial respiration and enzymatic activities were used to assess the development of soil microbial communities in two early ecosystems: along a 99 year glacial chronosequence, and in reconstructed soils in the Canadian boreal forest following open-pit mining. In the glacial environment, microbial biomass, respiration and enzymatic activity increased along the chronosequence and became more similar to the reference stand as vegetation developed. Further, in mid-successional stage soils, microbial biomass in plant rhizospheres was double that measured in bulk soil. In the reconstructed soils the use of organic amendments originating from the target ecosystem placed both the vegetation and soil microbial community on a faster trajectory towards ecosystem recovery than did the use of alternative amendments.