Understanding how the effects of land use change on plant communities affect soil microbial communities remains a key challenge in ecology, especially in tropical forests where logging has strongly modified tree species composition. We investigated the impact of logging on soil microbial assemblages and determined the influence of tree community composition, community-weighted mean (CWM) tree traits and soil properties as determinants of soil microbial community structure in old-growth (OG) and selectively-logged (SL) forests across Malaysian Borneo. Whilst bacteria and protistan communities were similar between OG and SL forest, fungal communities were distinct. Logging led to more homogeneous ecto (EcM) and arbuscular (AM) mycorrhizal communities and reduced the relative abundance and diversity of EcM fungi. Microbial community composition was best predicted by soil properties, followed by plant traits. Tree community characteristics explained additional variation in fungal communities, whilst the basal area of EcM host trees positively and negatively associated with the relative abundance of EcM and AM fungi respectively. These findings demonstrate the importance of logging-induced changes in forest vegetation in shaping soil microbial communities and highlight the sensitivity of soil fungal communities to logging disturbance. These finding are significant as shifts in soil fungal communities can have wider implications for forest soil C cycling and storage. They also likely control the rate and extent of forest recovery and may be important to inform management strategies for tropical forest restoration.