Little is known about the effects of temperature and drying–rewetting on soil phosphorus (P) fractions and microbial community composition in regard to different fertilizer sources. Soil P dynamics and microbial community properties were evaluated in a soil not fertilized or fertilized with KH₂PO₄ or swine manure at two temperatures (10 and 25 °C) and two soil water regimes (continuously moist and drying–rewetting cycles) in laboratory microcosm assays. The P source was the dominant factor determining the sizes of labile P fractions and microbial community properties. Manure fertilization increased the content of labile P, microbial biomass, alkaline phosphomonoesterase activity, and fatty acid contents, whereas KH₂PO₄ fertilization increased the content of labile inorganic P and microbial P. Water regimes, second to fertilization in importance, affected more labile P pools, microbial biomass, alkaline phosphomonoesterase activity, and fatty acid contents than temperature. Drying–rewetting cycles increased labile P pools, decreased microbial biomass and alkaline phosphomonoesterase activity, and shaped the composition of microbial communities towards those with greater percentages of unsaturated fatty acids, particularly at 25 °C in manure-fertilized soils. Microbial C and P dynamics responded differentially to drying–rewetting cycles in manure-fertilized soils but not in KH₂PO₄-fertilized soils, suggesting their decoupling because of P sources and water regimes. Phosphorus sources, temperature, and water regimes interactively affected the labile organic P pool in the middle of incubation. Overall, P sources and water availability had greater effects on P dynamics and microbial community properties than temperature.