Background <p>Phosphorus is an essential nutrient for plants that maintains global ecological balance. The core of its biogeochemical cycle lies in the interaction between soil, plants, and microorganisms. In the soil environment, microorganisms are the key force driving phosphorus nutrient availability. By converting phosphorus forms, they directly regulate the process of phosphorus supply from soil phosphorus reserves to plants.</p> Aims <p>This article comprehensively examines the pathways and influencing factors of soil phosphorus cycling, systematically analyzing the role of microorganisms within this process. As integral components of agricultural ecosystems, soil microorganisms significantly regulate phosphorus availability through rapid transformation—via absorption, assimilation, and release—of diverse phosphorus forms. However, the application of microbial agents to enhance phosphorus bioavailability faces persistent challenges. These include weak microbial colonization capacity, limited environmental adaptability, and insufficient broad-spectrum interactions between crops and microorganisms. Consequently, we systematically analyze the bottlenecks hindering microbial agent efficacy in soil phosphorus mobilization. To address these limitations, we propose a compatibility framework centered on “plant–microbe-soil” synergy. Through the optimization of microbial application technology, its function in the phosphorus transformation process can be effectively enhanced, thus promoting the sustainable use of phosphorus resources in agricultural production, maintaining the dynamic balance of the soil phosphorus cycle, and at the same time protecting the safety of food production and the green sustainability of the ecological environment.</p>