Aims <p>Organic fertilization is considered an effective method for improving soil quality. This study investigated the changes and interactions among soil quality, fungal diversity, and network complexity across a gradient of manure application rates at the northeastern margin of the Qinghai-Tibet Plateau.</p> Methods <p>We conducted a field experiment with well-rotted sheep manure in subalpine meadows, including six application rates (2,250–9,750&#xa0;kg&#xa0;ha⁻¹) and unfertilized control. The soil quality index (SQI) was calculated based on physicochemical properties, and soil fungi were analyzed via high-throughput sequencing.</p> Results <p>Medium manure application (6,650&#xa0;kg&#xa0;ha⁻¹) significantly enhanced soil quality (SQI + 78.51%) and aboveground biomass. Segmented regression analysis identified a threshold of 5,996&#xa0;kg&#xa0;ha⁻¹ for soil quality response, with an optimal fertilization range of 4,923–6,965&#xa0;kg&#xa0;ha⁻¹. Manure application significantly altered fungal diversity and network complexity, with the most pronounced effects observed on rare taxa. Variance partitioning analysis revealed that fungal diversity contributed more to soil quality than network complexity. Mixed-effects models further demonstrated that the diversity of intermediate taxa and the network complexity of rare taxa had significant non-linear effects on soil quality.</p> Conclusions <p>This study quantified the nonlinear response of subalpine meadow soil quality to manure application on the Tibetan Plateau, establishing optimal ranges and a critical threshold. Soil quality improvement was primarily driven by fungal diversity but involved an ecological trade-off: shifts in intermediate fungal diversity and rare-taxa network complexity. These findings underpin precision nutrient management and highlight the need to consider hidden ecological costs when managing soil microbiota.</p>