Purpose Zinc (Zn) deficiency in soils and crop plants is a global concern, undesirably influencing crop productivity, crop quality and human health. Farmers add Zn to soil through different agro-inputs by various means, which influences its behaviour in soil-plant systems. Efficient soil Zn management by estimating soil Zn fractions and assessing their contribution towards phyto-availability of Zn, crop yield and crop Zn uptake is therefore crucial for achieving sustainable crop yield. Methods We carried out the present study to assess the impact of different nutrient management practices (NMP) for 20 years on yield, Zn uptake by maize (Zea mays L.), and Zn distribution in Vertisol. The NMP practices consisted of different levels of nitrogen (N) - phosphorus (P) - potassium (K) supplied through inorganic fertilizers and various organic materials such as farmyard manure (FYM), poultry manure, urban compost, maize residue, Gliricidia sepium loppings alone or in combination. Results Application of 5 Mg FYM ha(-1) along with 75% of soil-test-crop response (STCR) based NPK resulted in highest grain and stover yield. Zinc content and uptake by maize grain varied significantly, and ranged from 19.6 to 29.3 mg kg(-1) and from 34.2 to 167 g ha(-1), respectively under different treatments. Annual addition of 20 Mg FYM ha(-1) recorded the highest soil organic carbon content of 8.94 g kg(-1). Addition of 1 Mg poultry manure ha(-1) with 75% STCR based NPK, 5 Mg urban compost ha(-1) with 75% STCR based NPK, and 2 Mg Gliricidia sepium loppings ha(-1) along with 5 Mg maize residue mulch ha(-1) and 5 Mg FYM ha(-1) to soil recorded relatively higher levels DTPA-Zn of 2.48, 2.32 and 2.18 mg kg(-1), respectively. Different treatments significantly influenced sorbed (Sorb-Zn), easily reducible Mn bound (ERMn-Zn), carbonate bound (Carb-Zn), organic matter bound (OM-Zn), Fe and Al oxide bound (FeOX-Zn) and residual (Res-Zn) Zn in soil. Zinc fractions in soil across the different treatments followed the order: Res-Zn (similar to 71- 81%) > ERMn-Zn (similar to 9.48-11.9%) > Sorb-Zn (similar to 3.16-5.32%) > FeOX-Zn (similar to 2.61-7.38%), Carb-Zn (similar to 2.35-3.67%), OM-Zn (similar to 0.19-0.64%), and water-soluble Zn (WS-Zn) (<= 0.19%). DTPA-Zn was positively and significantly correlated with WS-Zn, Sorb-Zn, ERMn-Zn, Carb-Zn, OM-Zn and FeOX-Zn. Path coefficient analysis revealed direct effect of Sorb-Zn, ERMn-Zn and Carb-Zn on Zn uptake by maize crop. Conclusion Integrated use of organic and inorganic sources of nutrients (5 Mg FYM ha(-1) + 75% of STCR based NPK) found to be superior for achieving higher maize yield and soil Zn availability. Various Zn fractions contributed Zn fractions towards Zn availability in soil, yield, Zn content and uptake by maize. This information is useful for managing Zn in soil-plant systems for higher yield and Zn uptake by maize under different nutrient management scenarios.