Background and Aims <p>The activity of overpopulated ungulates can alter soil properties, thereby generating an indirect “legacy effect” on tree seedlings. Soil microbes are likely to play important roles in these effects through shifts in processes such as decomposition and nitrification, yet their contributions remain understudied. In particular, functional groups of mycorrhizal fungi differ in their soil nitrogen (N) requirements, suggesting that legacy effects on tree seedling performance (growth, mortality, and disease occurrence) may depend on mycorrhizal association.</p> Methods <p>In a cool-temperate forest in Japan, we investigated the role of soil microbes, especially arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, in the legacy effects of sika deer (<i>Cervus nippon</i>) overpopulation. We compared plant and soil properties between deer-fenced plots (6–7&#xa0;years protected from deer) and control plots (6–7&#xa0;years under deer overpopulation) through seedling surveys and soil sampling, and also conducted a potted seedling transplant experiment. During the study, tree seedlings in the control plots were protected from direct deer impacts using nets.</p> Results <p>We found that ECM seedlings showed reduced mortality in control plots, likely driven by greater ECM fungal dominance in these soils. In contrast, AM seedlings showed reduced growth in control plots, likely due to the decrease in soil nitrate concentrations in these soils, combined with their greater dependence on inorganic N relative to ECM seedlings.</p> Conclusion <p>Our study demonstrates that considering tree mycorrhizal associations is critical for predicting the legacy effects of ungulate overpopulation on plant community recovery trajectories.</p>