It is becoming well‐established that plant diversity is instrumental in stabilizing the temporal functioning of ecosystems through population dynamics and the so‐called insurance or portfolio effect. However, it remains unclear whether diversity–stability relationships and the role of population dynamics in soil microbial communities parallel those in plant communities. Our study took place in a long‐term land management experiment with and without perturbation to the soil ecosystem by tilling. We assessed the impacts of the soil perturbation on the diversity, synchrony and stability relationships in soil fungal and bacterial communities. We found that the perturbation to the soil ecosystem not only reduced the abundance and richness of the fungal community, but it also reduced the temporal stability in both bacterial and fungal abundance. The fungal community abundance was destabilized by soil tilling due to reduced richness and increased temporal variation in individual taxa. In contrast, soil tilling destabilized the bacterial community abundance by reducing the temporal variation in individual taxa. Both bacterial and fungal community abundances were more temporally variable when taxa fluctuated more synchronously through time. Our results show that land management practices, such as tilling, can destabilize soil microbial abundance by reducing the richness and disrupting the temporal dynamics below‐ground. However, the differences in the mechanisms that underlie the temporal variations in fungal and bacterial net abundances suggest that the mechanisms that drive the stability can differ among guilds of organisms within the same system. The different temporal responses between the fungal and bacterial communities are likely linked to changes in edaphic properties resulting from the physical alteration of the soil structure.