Aims <p>Microbial dormancy is a fundamental ecological strategy that governs soil microbial persistence, functional stability, and the capacity of microbial communities to respond to environmental change. However, how agricultural management practices influence the soil microbial dormancy remains insufficiently understood.</p> Methods <p>To address this knowledge gap, we conducted a long-term field experiment involving three nitrogen fertilization levels and four cover crop treatments to evaluate their effects on soil microbial dormancy. Random forest and variance partitioning analyses were used to identify the key environmental drivers of microbial dormancy.</p> Results <p>Our results demonstrated that that nitrogen fertilization reduced the soil microbial dormant fraction, with a significant decrease observed under N120 treatment (120 kg N ha⁻¹), where dormancy declined by 7.3% relative to the N0 treatment (0 kg N ha⁻¹). Meanwhile, ammoniacal nitrogen become the key predictor of microbial dormancy, exhibiting a significant negative relationship with the soil microbial dormant fraction. Cover crops effects were management dependent: the soybean-Sudan grass mixture (SS) significantly reduced the microbial dormant fraction by 5.4% relative to no cover crops, whereas monoculture cover crops showed no significant effect. In the mixed cover system, ammoniacal nitrogen was identified as the primary factor of microbial dormancy and showed a significant negative correlation.</p> Conclusions <p>Our findings emphasize the pivotal role of soil microbial dormancy in mediating microbial responses to cropland management, offering a new perspective for linking nutrient inputs with microbial functioning and improving new insights for designing management strategies that promote resilient and functionally stable agricultural soils.</p>