Maintaining an adequate phosphorus (P) supply for plants and microorganisms is central to agricultural production; however, the long-term effects of organic manure and inorganic fertilizer application on soil P cycling remain unclear. Organic P cycling in a sandy loam soil receiving medium and high rates of farmyard manure (FYM) with and without mineral fertilisers was studied in a long-term field experiment with 14C/33P isotope labelling and metagenomic shotgun sequencing. FYM application alone negatively affected soil total P and organic P (Po) accumulation by enhancing crop offtake, enhancing Po mineralisation and stimulating P loss from the topsoil by reducing its P sorption potential. The P mineralisation/immobilisation rates detected by the 33P pool dilution method were significantly correlated with the abundance of microbial P cycling genes. Soil available C and N concentrations were related to gross P mineralisation/immobilisation rates and the abundance of P uptake/scavenging genes. Microbial genes related to P uptake and metabolism were more abundant than P scavenging genes, while P scavenging genes may work efficiently as both of them can sustain similar P mineralisation and immobilisation rates. The addition of FYM also promoted phosphatase activity reflecting the increased supply of Po in these soils. Our study demonstrates that long-term FYM application alters soil Po stocks and cycling, and that microbial functional gene abundance was coupled with P cycling rates.