Background and Aims <p>Atmospheric nitrogen (N) deposition is the main driving factor of global climate change affecting the stability and function of forest ecosystems. Understory vegetation and soil microbial communities are essential components in forest ecosystems. However, previous studies have largely examined the effects of either vegetation or soil microorganisms on soil multifunctionality (SMF) separately, while the integrated roles of aboveground and belowground biota remain unclear.</p> Methods <p>We conducted a 15-year N addition experiment in a temperate forest to assess how N inputs affected understory vegetation and soil microbial diversity and their roles in SMF.</p> Results <p>Our results showed that N addition significantly reduced the <i>α</i>-diversity of both understory vegetation (<i>P</i> &lt; 0.0001) and soil microorganisms (<i>P</i> &lt; 0.005), and led to a decline in SMF. Structural equation modeling indicated that N addition indirectly inhibited SMF by decreasing soil pH and altering biodiversity, rather than exerting a direct effect. Microbial diversity—especially bacterial <i>α</i>-diversity—played a significant role in driving SMF. In contrast, understory vegetation diversity exhibited a nonlinear association with average SMF and had a significantly negative effect on SMF at lower thresholds (e.g., 20%). Moreover, long-term N inputs weakened the linkage between above-ground and belowground communities.</p> Conclusion <p>These findings highlighted bacterial diversity was a key regulator of multifunctionality under N addition, and further offered new insights into biotic mechanisms that maintain ecosystem function under anthropogenic nutrient inputs. Our results also provide a theoretical basis for the sustainable management of temperate forests experiencing increasing nitrogen deposition.</p>