Nutrient constraints in salt-affected soils are one of the limiting factors for crop production. We investigated phosphorus (P) availability to wheat crop and its correlations with different fractions of P in salt-affected soils in response to various phosphatic fertilizer’s application. Three different types of soils having electrical conductivity of soil extract (ECe) < 4 dS m−1 and sodium adsorption ratio (SAR) < 13.2 (mmol L−1)1/2, ECe 8 dS m−1 SAR 20 (mmol L−1)1/2 and ECe 12 dS m−1 and SAR 30 (mmol L−1)1/2 were used for this experiment. Different P fertilizers viz. control, diammonium phosphate (DAP), single super phosphate (SSP) and nitrophos (NP) were applied on these soils. The doses of nitrogen, phosphorus and potassium were remained same for all the treatments. The P fractions, agronomic parameters and P-availability to plants were determined. Results indicated increase in shoot dry weight (61%) and photosynthetic rate (9%) in SSP treated soil at EC 8 dS m−1 and SAR 20 (mmol L)1/2. The total P (7.6%) in soil and respiration rate (1.9%) in plant was recorded maximum in DAP treated soil at EC 8 dS m−1 and SAR 20 (mmol L)1/2, and membrane stability index (44%) in plant shoot, extractable P (23%) in soil and P concentration (22%) in shoot were recorded maximum in SSP treated soil at EC 12 dS m−1 and SAR 30 (mmol L)1/2. It was concluded that SSP fertilizer perform better in salt-affected soil for growth and yield of wheat compared to other phosphatic fertilizers.