With increasing emphasis on sustainable agricultural practices, understanding their long-term impacts on crop productivity, resource-use efficiency and environmental sustainability has become essential. The experiment was conducted at Krishi Vigyan Kendra, Jammu during the rabi seasons from 2020–21 to 2024–25 to evaluate the long-term effects of sustainable farming systems on carbon budgeting, energy indices and productivity of different wheat varieties under the subtropical conditions of Jammu region. The study was laid out in a factorial randomised block design with 3 replications comprising 12 treatment combinations. Two factors were evaluated: the first factor consisted of four wheat varieties (JAUW-584, JAUW-672, DBW-222 and HD-3237) whereas the second factor included integrated nutrient management (INM), organic farming and natural farming. The results revealed that the wheat variety HD-3237 under INM recorded higher dry matter accumulation, grain yield, yield sustainability index, production efficiency, nutrient uptake, carbon sustainability index, net returns and benefit-cost ratio along with the lowest carbon footprint. In contrast, HD-3237 under organic farming exhibited higher soil organic matter, greater carbon sequestration and the lowest bulk density. Among the energy indices, HD-3237 under natural farming recorded the highest energy productivity and energy-use efficiency along with the lowest input energy requirement. Overall, the wheat variety HD-3237 under INM recorded the highest grain yield, nutrient uptake, carbon sustainability index and benefit-cost ratio. However, HD-3237 under organic farming resulted in higher soil organic carbon and carbon sequestration whereas the same variety under natural farming recorded the highest energy productivity and energy-use efficiency.