A healthy soil plant continuum is critical for maintaining agroecosystem functions and ensuring food security, which is the basis of sustainable agricultural development. Diverse soil microorganisms form a complex assembly and play an important role in agroecosystems by regulating nutrient cycling, promoting plant growth, and alleviating biotic and abiotic stresses. Improving microbial coexistence may be an effective and practical solution for the promotion of soil–plant ecosystem health in the face of the impacts of anthropogenic activities and global climate change. Modern coexistence theory is a useful theoretical framework for studying the coexistence of species that are competing for resources. Here, we briefly introduce the basic framework of modern coexistence theory, including the theoretical definitions and mathematical calculations for niche difference and fitness difference, as well as ways to test for these differences empirically. The possible effects of several major biotic and abiotic factors, such as biological interactions, climate change, environmental stress, and fertilization, on microbial niche and fitness differences are discussed. From the perspective of stabilizing and equalizing mechanisms, the potential roles of microbe–microbe interactions and plant–microbe interactions in promoting healthy soil–microbe–plant continuum are presented. We suggest that the use of the coexistence theory framework for the design and construction of microbial communities in agricultural production can provide a solid basis for the biological improvement of agroecosystems.