A field experiment was conducted to study the long-term effects of nutrient management practices on micronutrient concentrations in soil and their uptake by crops under a long-term rice–wheat cropping system. The treatments comprised different combinations of N, P, K, Zn and farm yard manure (FYM), used as nutrient management practices. After 25 years of continuous cropping, the higher grain yields and uptake of iron (Fe), manganese (Mn), copper (Cu) and zinc (Zn) were obtained when FYM was applied along with mineral sources of nitrogen, phosphorus and potassium (NPK) when compared to mineral sources of NPK alone. The residual effect of FYM, applied to rice, on the yield of subsequent wheat was significant. The application of mineral NPK with FYM recorded higher diethylene triamine penta acetic acid extracted (DTPA)-Fe, Mn and Cu concentrations in the soil compared to any other treatment. The plots with Zn application showed higher DTPA-Zn concentration in the soil compared to any other treatments. The available Fe, Mn and Cu in the soil were higher than their critical limits and the soil was low in Zn where inorganic fertilizers were applied alone (without Zn). Integrated application of mineral NPK and FYM to the rice crop and mineral NPK to wheat was found to be the best nutrient management practice in producing higher yields of rice and wheat and improve long-term soil micronutrient concentrations.