In a field experiment initiated in 1991 kharif season (April–October) on an acidic soil in the Western Himalayas of India, 25% and 50% of the recommended doses of nitrogen were substituted through different organics, viz. farmyard manure (FYM), wheat cut straw and Sesbania aculeata (as green manure) in rice, followed by use of chemical fertilizers in wheat each year. The aim of this work was to study the long-term integrated effect of organics and chemical fertilizers on grain yield of rice–wheat system and soil quality. Based on five years’ moving average values, continuous cropping without fertilization or manuring (control) gave the lowest grain yields of both rice and wheat. Application of 50% N through FYM plus 50% NPK through chemical fertilizers to rice followed by 100% NPK through chemical fertilizers to wheat (T3) maintained the highest productivity of rice and wheat at about 3.4 Mg ha−1 and 3.3 Mg ha−1, respectively, as found from the pooled grain yield over the years. The highest values of organic carbon, cation exchange capacity and available N, P, K were also recorded under this treatment (T3). Soil pH was marginally affected by different treatments, while Diphenyl Triamine Penta Acetic acid extractable micronutrient cations increased over control when chemical fertilizers were applied in conjunction with different organics.