Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.