Abstract: This study focused on pure stands of Paulownia spp., Pinus massoniana, Cunninghamia lanceolata, and mixed Paulownia-conifer stands. It used substrate-induced respiration (SIR) and phospholipid fatty acid (PLFA) analyses to compare the effects of relatively fertile brown soil and poor sandy ginger black soil on soil microbial community function and structure. Results indicated that the impact of stand type on microorganisms was significantly dependent on habitat conditions. In the nutrient-poor habitat, compared to pure Paulownia stands, both pure conifer stands and their mixed stands with Paulownia significantly decreased microbial basal respiration and biomass, and increased PLFA-derived physiological stress indicators, with pure C. lanceolata stands exhibiting the most pronounced inhibitory effect. No significant differences were found among the different stand types in the fertile habitat. In contrast, microbial specific respiration (qO₂) and PLFA-derived stress indicators under pure Paulownia stands showed less fluctuation across different habita, indicating a relatively high level of stability. With microbial activity and biomass decreasing with depth, and the impact patterns of stand type and habitat varying across soil layers. Microbial community structure was primarily determined by soil nutrient status, with stand type exerting a significant regulatory effect. In nutrient-poor habitats, pure conifer stands and mixed Paulownia-conifer stands may impair key ecological functions mediated by soil microorganisms through inhibiting microbial activity and biomass. In fertile habitats, the influence of tree species selection on these microbial indicators was relatively limited. The relative stability of microbial responses to environmental changes under Paulownia spp. stands may be associated with their sustained root-derived carbon inputs.