Phosphorus (P) fractions and their availability in soils can be affected by long-term nitrogen (N) fertilizer application, which can subsequently affect plant growth and productivity. The extent of P fxation at different N fertilization rates is still unclear and this study highlighted an appropriate N fertilization rate showing minimum P fxation and higher P content uptake by the plants. Paradox changes of P into various organic (Po) and inorganic (Pi) fractions and their contribution in P content uptake and yield was evaluated under long-term (12 year) application of different N rates (0, 80, 160, 240, and 320 kg N ha− 1, hereafter, N0, N80, N160, N240, and N320, respectively) in winter wheat (Triticum aestivum L.). Phosphorus fractions were measured using Tiessen and Moir fractionation scheme modifed from Hedley method. N rates signifcantly decreased available (especially NaHCO3-Pi) and residual fractions of P, when compared with N0. The NaHCO3-Pi showed a signifcant positive relationship with total plant P content and grain yield. Grain yield was maximum in N160 treatment with no signifcant difference between N160 and higher N levels. Increase in N rates from N0 to N320 little increased organic P fractions; NaHCO3-Po increased from 64.0 to 69.7 mg kg− 1, HCl-Po increased from 60.5 to 87.1 mg kg− 1, but NaOH-Po decreased from 46.5 to 31.2 mg kg− 1. All Pi fractions increased, and maximum contents were observed for HClD- -Pi fraction ranging between 189–265 mg kg− 1 from N0 to N320 treatments. HClD-Pi fraction was highest contributor (39%) in total P, which is transformable into available P with time. A decrease in residual P by 7.4% was observed in N320 compared with N0 treatment. Residual P fraction was positively correlated with grain yield, biomass, total P content uptake, and with the moderate available fractions (NaOH-Pi, NaOH-Po, and HClD-Pi). It can be concluded that excessive N fertilization does not always result in increased crop yield but can increase P fxation (HClD-Pi form) and decreases residual P contents. Therefore, optimum N fertilization should be applied keeping in view the crops requirement. This study advocates that N application at 160 kg N ha− 1 can maintain higher wheat yield (5844 kg ha− 1) in Loess Plateau, with no signifcant increases in P fxation and loss of residual P