The aim of the present study was to evaluate the transformation of applied inorganic phosphorus (P) in highly calcareous soils under two moisture regimes. The experimental design was a factorial combination of two rates of P (0 and 300 mg P kg–1 as KH2PO4) and two moisture regimes (field capacity, FC; waterlogged, WL) in a completely randomised design in duplicate with 20 surface soil samples. The fractionation sequence of inorganic P included successive extraction with NaHCO3, NH4 acetate buffer (NH4OAc), MgCl2, NH4F, NaOH–Na2CO3 (HC), Na citrate–bicarbonate–dithionite (CBD), and H2SO4 carried out 80 and 160 days after incubation. Recovery of applied P in each fraction was calculated as the difference between samples treated and untreated with P. Results indicated that NaHCO3-P decreased from 80 to 160 days, and the decrement was higher under WL than FC moisture regime. The NH4OAc-P was lower under WL than FC at 160 days, while P associated with free and crystalline Fe and Al oxides (NH4F-P, HC-P, CBD-P) was higher under WL than FC for both incubation periods. Oxalate-, citrate-, and citrate–ascorbate-extractable iron under FC and in conjunction with oxalate- and CBD-extractable aluminium and quinone- and hydroxylamine–hydrochloride-extractable manganese were the most influential factors regulating all P fractions. Results of the present study revealed that transformation of applied P into Al- and Fe-P fractions is not as low as previously reported in highly calcareous soils and that Al- and Fe-P oxides may be important in P transformation of these soils, especially in waterlogged condition.