National-scale nitrogen budgets reveal large inefficiencies in Indian agriculture

India has pledged to halve nitrogen (N) waste by 2030, but a comprehensive system-scale budget is required to identify existing inefficiencies in agricultural N use. Here, we present an Environmentally Extended Input–Output model that leveraged data from literature and institutional repositories to quantify N inputs, flows, and losses across cropland, livestock, and aquaculture sectors. Estimated nitrogen use efficiency in 2020 varied for cropland (56%), aquaculture (20%), and livestock (8%). Only 50% of the applied agriculture N was converted to useful products (food, feed, fuel, non-food); while the rest was lost as Nr (17% NH₃, 16% runoff, 7% leaching, 5% NOx, 1.5% N2O). Quantified emission estimates have high uncertainties (<±54%) due to limitations in the underpinning activity and emission factors data. Findings suggest that while current production meets N demand, reducing Nr losses will require integrated agricultural-nutrition policies and improved production efficiencies to reconcile India’s food production and environmental sustainability. India’s agriculture converts only half of nitrogen inputs into products, with substantial losses to air and water and especially low efficiency in livestock and aquaculture, based on an environmentally extended input-output analysis of nitrogen flows across multiple sectors.