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Jatropha curcas is a potential biofuel crop and press cake is an important co-product obtained during biodiesel production. In order to assess the long-term effects of application of Jatropha press cake on soil quality parameters and to evaluate its efficacy as an organic manure, a field trial was carried out in degraded wasteland of Gujarat, India with four treatments chosen on the basis of equivalent amounts of N supply through urea, Jatropha press cake, farmyard manure (FYM) and half dose of urea. The activities of various exocellular enzymes involved in nutrient cycling, microbial biomass carbon, respiration, fluorescein diacetate (FDA) hydrolysis and the influence of chemical composition of the organic manures on these parameters were studied following seven continuous years of application of nutrient amendments. Degradation of the phorbols, toxins present in press cake, was also studied. Except for acid phosphomonoesterase, enzyme activities were higher in FYM compared to other treatments. Lignin content was higher in FYM while the ligno-cellulosic fraction was higher by 45% in press cake as compared to FYM. Notably, carbon accumulation in soil was higher per unit of applied carbon in press cake treated soil. Ratio of microbial biomass carbon to soil organic carbon was higher in press cake amended soil. Phorbol esters were degraded to negligible amounts. The increase in yield of Jatropha following improved enzyme activities, microbial carbon and FDA hydrolysis owing to press cake application in erstwhile poor soils unequivocally establishes the scope of Jatropha press cake in reclaiming unfertile wastelands sustainably.