Present field experiment was conducted at the Indian Institute of Soil Science, Bhopal on a clayey soil (Typic Haplusterts) during 2012–13 and 2013–14. The performance of soybean (Glycine max, cv. JS 335)–wheat (Triticum durum, cv. HI 8498) cropping system in terms of yield, nutrient uptake and economics under different organic and inorganic nutrient was assessed. The experiment was laid out in a randomized block design with seven treatments in four replications. The treatments involved different nutrient inputs viz. organic manure (OM) (T1); biodynamic preparation (BD) (T2); OM + panchagavya (OM + PG) (T3); OM + BD (T4); OM + PG + BD (T5); control (T6); and recommended dose of fertilizers (RDF) (T7). Cattle dung manure on N equivalent basis to soybean in kharif and cattle dung manure (CDM) + vermicompost (VC) + poultry manure (PM) (1:1:1 on N equivalent basis) to wheat were applied as organic manure whereas nutrients were supplied in the form of chemical fertilizers in RDF treatment. The yield of soybean and wheat crops obtained with organic combinations were found comparable and even better (5–13% higher) with those obtained under RDF which enhanced nutrient removal by soybean and wheat crops. The soybean–wheat sequence registered an increment of 2–11% and 11–26% in total N and P uptake, respectively over RDF. The net returns obtained under organic treatments were found statistically at par with those obtained under RDF.