Soil microbiomes drive key functions in agroecosystems, determining soil fertility, crop productivity and stress tolerance. The microbiome is intricately linked with soil structure, such as aggregation and pore connectivity, because this structure regulates the flow of water, oxygen and nutrients through the system. In this Review, we summarize the key functions of soil microbiomes in agroecosystems, highlight the dependence of these functions on the structural integrity of the soil, and discuss how agricultural practices influence the link between soil structure and microbiome functioning. System-level agricultural management practices can induce structural alterations to the soil, thereby changing the microbial processes occurring at the microscale. These changes have large-scale consequences, such as soil erosion, reduced soil fertility and increased greenhouse gas emissions. Sustainable approaches such as integrated soil fertility management and integrated pest management seek to improve soil structure and enhance microbial biodiversity, but we lack a mechanistic understanding of how multifaceted decisions at the farm level shape these context-dependent small-scale processes in the long term. Future research needs to bridge the microscale and field scale to inform agricultural management decisions for building climate-smart, resource-efficient and stress-resilient agroecosystems, and to harness the soil microbiome as a nature-based solution for sustainable agriculture.