Major nutrient management systems for rice-wheat cropping were compared for their potential to credit organic carbon (C) to the soil, its fractionation into active (very labile, VLc; labile, Lc) and passive (less labile, LLc; non-labile, NLc) pools, and crop yield responses. A ten-year long experiment was used to study effects of: (i) no inputs (Control, O), (ii) 100% inorganic fertilizers (F) compared to reduced fertilizers inputs (55%) supplemented with biomass incorporation from (iii) opportunity legume crop (Vigna radiata) (LE), (iv) green manure (Sesbania aculeata) (GM), (v) farmyard manure (FYM), (vi) wheat stubble (WS), and (vii) rice stubble (RS). Maximum C input to soil (as the percentage of C assimilated in the system) was in GM (36%) followed by RS (34%), WS (33%), LE (24%), and FYM (21%) compared to O (15%) and F (15%). Total C input to soil had a direct effect on soil C stock, soil C fractions (maximum in VLc and LLc), yet the responses in terms of biological yield were controlled by the quality of the biomass (C:N ratio, decomposition, etc.) incorporated. Legume-based biomass inputs accrued most benefits for soil C sequestration and biological productivity.