Intensive farming with high yielding cultivars, application of high analysis NPK fertilisers, and reduced use of organic manures caused a decrease in the availability of zinc (Zn) in Indian soils. We collected soil and plant samples from an ongoing long-term experiment at Indian Agricultural Research Institute, New Delhi, to study the distribution of different fractions of Zn in an Inceptisol and their contribution towards the Zn availability in soil and Zn uptake in maize–wheat crop rotation. The treatments used for the study were NPK, NPK + FYM, NPK + Zn, and control (no fertiliser or manure). The DTPA-Zn concentration in soil was higher where Zn had been applied and declined with an increase in soil depth. The distribution of different fractions of Zn under various treatments and depths was inconsistent, and varied in a cropping year. The average concentration of total Zn (mg/kg) was 183, 183, 171, and 211 in 0–0.15, 0.15–0.30, 0.30–0.45, and 0.45–0.60 m depth, respectively. Residual Zn was the dominant portion of total Zn at all soil depths. Grain and stover yield of maize ranged from 1.10 to 2.43 t/ha and 1.22 to 2.46 t/ha, respectively, under different treatments, whereas, the yield of wheat grain varied from 2.25 to 4.69 t/ha and that of wheat straw from 2.56 to 5.20 t/ha. Highest uptake of Zn by both the crops occurred in Zn-treated plots. Zinc associated with easily reducible manganese, carbonate and iron and aluminum oxides contributed directly towards DTPA-extractable Zn. Sorbed Zn (SORB-Zn) and Zn associated with organic matter (OM-Zn) contributed significantly towards Zn uptake by the 2 crops.