Soybean (Glycine max (L.) Merr.)–wheat (Triticum aestivum L.) is the dominant cropping system in the Vertisols of central India due to congenial climate, development of agro-industries, and export opportunities. Both are high-value crops, and raising them using organics may further improve produce quality and help in sustaining long-term productivity of the system. Information is lacking on how to sustain the system with the sole use of organics or biofertilisers in Vertisols. A long-term study was made during 1995–2002 at Indore, India, to evaluate the effectiveness of 3 organic manures [farmyard manure (FYM), poultry manure (PM) and vermicompost (VC) at varying rates] and biofertilisers (Azotobacter + phosphate solubilising bacteria) on productivity, grain quality, soil fertility, and profitability of a wheat–soybean cropping system. Grain yield of wheat was significantly increased with PM at 2.5–10 t/ha or FYM at 10–20 t/ha compared with the control. However, the highest productivity was obtained with PM at 10 t/ha, which even performed better than NPK, indicating that NPK fertilisers alone did not provide adequate and balanced nutrition for potential yield of the crop. Quality parameters of durum wheat, viz. protein content, hectolitre weight and sedimentation value, increased, while yellow berry content decreased significantly with PM at 2.5–10.0 t/ha compared with the control. Soybean yields were significantly influenced by the residual effect of organic manuring treatment applied to wheat. The treatment receiving PM at 10 t/ha produced the highest grain yield of wheat. However, this treatment could not produce a similar response in soybean yield due to production of excessive vegetative growth, adversely affecting grain yield. Superiority of PM over FYM, vermicompost and biofertilisers was evident in the overall profitability of the system. Various soil fertility parameters including chemical and biological properties showed conspicuous improvement over the initial status under the FYM and PM treatments. Microbial biomass C and activities of phosphatase and dehydrogenase were increased significantly with applications of manures. Sustainability yield index was maximum under PM at 5–10 t/ha, followed by NPK. Results suggested that application of PM at 5–10 t/ha to wheat was essential for improving productivity, grain quality, profitability, soil health, and sustainability of a wheat–soybean system.