In order to evaluate the effects of phosphorus (P) fertilizer and contaminations of lead (Pb) and zinc (Zn) on root Pb, Zn, and P concentrations, pyromorphite (Pb5(PO4)3Cl, F, OH)) formation in a calcareous soil, an experiment was conducted as factorial on the basis of completely randomized design with three replications under greenhouse and laboratory conditions with three factors of Pb at four levels (0, 200, 400, and 800 mg kg − 1 soil as Pb(NO3)2), Zn at three levels (0, 25, and 250 mg kg − 1 soil as ZnSO4. 7H2O) and P at three levels (0, 50, and 500 mg kg − 1 soil as Ca(H2PO4). 2H2O). At the end of the rice growth period, root Pb, Zn, and P concentrations were measured. The treatment of Pb800P500Zn250 was subjected to X-ray diffraction (XRD) analysis for pyromorphite formation. The results showed that application of P fertilizer resulted in reducing the average root Pb and Zn concentrations by 15 and 2%, respectively. The application of Zn fertilizer resulted in reducing the average root Pb and P concentrations by 13 and 6%, respectively. The XRD results showed the formation of poorly crystalline chloropyromorphite. Also, in Pb and Zn polluted soils, application of P fertilizer could decrease mobility and bioavailability of these metals and restrict their uptake by plant.