Restoring soil fertility in farming systems is essential to sustain a crop and its productivity. Thus, the present study was conducted to assess the residual effects of the combined application of fertilizers and manures on yield, concentration and uptake of nutrients in wheat under basmati rice-wheat cropping system. The treatments applied in the present study involve T1: control, T2: farmyard manure (15 t ha−1), T3: poultry manure (6 t ha−1), T4: press mud (15 t ha−1), T5: rice straw compost (6 t ha−1), T6: farmyard manure (15 t ha−1) + 50% recommended dose of nitrogen (RDN), T7: poultry manure (6 t ha−1) + 50% RDN, T8: press mud (15 t ha−1) + 50% RDN, T9: rice straw compost (6 t ha−1) + 50% RDN, T10: 75% RDN, T11: farmyard manure (15 t ha1) + 75% RDN, T12: poultry manure (6 t ha−1) + 75% RDN, T13: press mud (15 t ha−1) + 75% RDN, T14: rice straw compost (6 t ha−1) + 75% RDN, T15: 100% RDN. The residual effects of organic manures significantly improved the growth parameters and yield attributes. Among different residual treatments, the use of farmyard manure + 75% NPK showed maximum plant height (125.2 cm), number of tillers (68.0 m−1), chlorophyll content (45.0) and yield (50.84 q ha−1 for grain and 80.43 q ha−1 for straw, respectively). Additionally, the incorporation of farmyard manure + 75% RDN demonstrated the highest uptake of nitrogen, phosphorus and potassium in grain (7.37, 3.31 and 4.93 g ha−1, respectively) and straw (1.72, 1.05 and 12.63 g ha−1, respectively). The maximum zinc, copper, iron and manganese concentrations were observed to be 32.0, 3.1, 52.1 and 17.6 mg kg−1 in grain and 8.2, 2.1, 374.6 and 20.5 mg kg−1 in straw, respectively. Similarly, the highest uptakes were observed to be 67.6, 15.5, 263.8 and 89.6 g ha−1 in grain and 173.3, 16.8, 3026.9 and 170.6 g ha−1 in straw, respectively. Thus, the integrated application of farmyard manure with 75% RDN could be used to sustain wheat productivity and maintain soil fertility which otherwise deteriorates due to the sole application of inorganic fertilizers.