The excessive application of manure has caused a high load of phosphorus (P) in the North China Plain. Having an understanding of how manure application affects soil P changes and its transport between different soil layers is crucial to reasonably apply manure P and reduce the associated loss. Based on our 28-year field experiments, the compositions and changes of P species and the risk of P loss under excessive manure treatments were investigated, i.e., no fertilizer (CK), mineral fertilizer NPK (NPK), NPK plus 22.5 t ha−1 yr−1 swine manure (LMNPK), and NPK plus 33.75 t ha−1 yr−1 swine manure (HMNPK). Manure application increased the content of orthophosphate and myo-inositol hexaphosphate (myo-IHP), especially the orthophosphate content exceeded 95%. The amount of orthophosphate in manure and the conversion of organic P to inorganic P in soil were the main reasons for the increased soil orthophosphate. Compared with NPK treatment, soil microbial biomass phosphorus and alkaline phosphatase activity in LMNPK and HMNPK treatments significantly increased. Compared with NPK treatment, a high manure application rate under HMNPK treatment could increase the abundance of organic P-mineralization gene phoD by 60.0% and decrease the abundance of inorganic P-solubilization gene pqqC by 45.9%. Due to the continuous additional manure application, soil P stocks significantly increased under LMNPK and HMNPK treatments. Furthermore, part of the P has been leached to the 60–80 cm soil layer. Segmented regression analysis indicated that CaCl2–P increased sharply when Olsen-P was higher than 25.1 mg kg−1, however the content of Olsen-P did not exceed this value until 10 years after consecutive excessive manure application. In order to improve soil P availability and decrease the risk of P loss, the manure application rate should vary over time based on soil physicochemical conditions, plants requirements, and P stocks from previous years.
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