The sustainability of agricultural production systems is significantly threatened due to climate change and land degradation. Agricultural practices like conventional tillage with imbalanced fertilizers, and indiscriminate irrigation have serious environmental implications like higher greenhouse gas (GHG) emissions. Therefore, we assessed the three-year productivity, effectiveness of energy, and carbon (C) footprint of soybean-wheat system under different tillage techniques [zero-till fiat beds (ZTFB), conventional till-raised beds (CTRB), and conven-tional till-fiat beds (CTFB)], irrigation regimes [irrigation at 25%, 50%, and 75% depletion of available soil moisture (DASM)] and fertilizer rates [50% and 100% recommended rates of fertilizers (RRF). The study was conducted for three years in a fixed-field plots using split-split plot design with three replications. The results show that conventional till-raised bed (CTRB) recorded higher system crop productivity (9.5-15.2%), energy-efficiency (17.3), C-output (6424), C-efficiency (11.7), C-sustainability index (9.73), net-returns (1035 US$ ha-1) and the least C-footprints (0.19) over conventional till-fiat beds (CTFB) and zero till-fiat beds (ZTFB). Whereas, residue mulched ZTFB plots exhibited-24.2% higher system water productivity and consumed less energy (-77.0%) over others. Irrigation applied at 25% depletion of available soil moisture (DASM25%) led to higher system productivity (5.96 Mg ha-1), energy output (232.6 GJ ha-1), energy-efficiency (13.4) and C-output (6657.4 kg CE ha-1) compared to DASM75% and DASM50%. Interestingly, C-footprints increased with ZTFB while least C-footprints were found under CTRB and CTFB. Consequently, the adaptation of CTRB with optimal irrigation and fertilizers will be a viable alternative for achieving improved system production, energy efficiency with a lower C-footprint under semi-arid regions.