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High biodiversity aboveground tends to increase the stability of ecosystem functioning when faced with a changing environment. However, whether and how soil biota affect ecosystem stability is less clear. Here, we introduce a framework for understanding the effects of soil biota on variation in ecosystem functioning under environmental changes. We conclude that soil biota may be a neglected factor determining ecosystem stability through their direct and indirect effects on plant diversity, the net productivity of an ecosystem, and compensatory dynamics among plant species, and via altering ecosystem resistance and resilience. Furthermore, future research needs to consider that effects of soil biota on ecosystem stability will vary depending on extrinsic factors, and for a given perturbation and ecosystem function.