Carbon dioxide (CO 2 ) fluxes from agricultural soils have been considered as one of the important environmental impact issue, due to their role in global warming and also its mitigation by carbon (C) sequestration in soils. Substantial scope of C sequestration with the application of inorganic fertilizers and manures has been reported, but the long-term effects of continuous application need to be critically examined. To study the effect of continuous differential application of NPK fertilizers and farmyard manure (FYM) in maize-wheat cropping system, CO 2 fluxes were measured via closed chambers and gas chromatography in a long-term experiment in progress for the past 42 years. The average daily CO 2 fluxes differed significantly amongst various treatments and were 55, 26 and 92% higher in NPK, N and NPK + FYM treatments over the control in the maize crop season and 43, 8 and 83% in the wheat crop season. Highly significant correlation of CO 2 emissions was found with soil organic carbon and total nitrogen in the maize and the wheat crop seasons. Although, CO 2 emissions were higher from long-term inorganic fertilizers and FYM treatments, still they are environmentally sustainable management practices, as they increased soil fertility and crop yields which consequently resulted in higher atmospheric CO 2 capture by plants and carbon sequestration in soils.