Puddled transplanted rice followed by conventional till wheat, the most predominant cropping system in South Asia is unsustainable, highly energy intensive and leads to significant carbon equivalent emissions. Conservation agriculture (CA) practices like zero till dry direct seeded rice, zero till wheat, residue retention and diversified crop rotations have potential to improve productivity and reduce energy and carbon footprints. Therefore, we evaluated the energy and carbon relationships in rice-wheat cropping system under contrasting tillage and residue management scenarios with the aim to promote sustainable and energy efficient CA systems with lower C footprint. Treatments comprised of zero till dry direct seeded rice – zero till wheat (~double zero till) and zero till dry direct seeded rice – zero till wheat – zero till mungbean (~triple zero till) systems, with and without residue retention of preceding crop. Besides, conventional till (CT) rice (i.e. puddled transplanted rice) – CT wheat system (~CTRW), and conventional till rice – zero till wheat system were adopted as farmers’ practice control. Two-year pooled results highlighted that the zero till (ZT) systems led to consumption of substantially lower operational energy for land preparation (100 %), sowing (34–50 %) and irrigation (24–36 %) than conventional till system. The zero till direct seeded rice + mungbean residue – zero till wheat + rice residue – zero till mungbean + wheat residue system (~ZTRWMb+R) registered ~5 % lower rice yield but 16 % and 23 % higher wheat grain yield and system biomass yield, respectively over CTRW. This system incurred highest total input energy (157.4 × 103 MJ ha−1), having ~64 % of this energy shared from renewable crop residue, but had highest (11.3) energy use efficiency from non-renewable resources (fuel, fertilizers, machinery). In contrast, the zero till direct seeded rice – zero till wheat – zero till mungbean system without residue resulted in highest net energy returns, energy ratio, energy productivity and energy intensity. The ZTRWMb+R system led to 64 % lower yield scale C footprint (304 kg CO2-eq. t−1) compared to CTRW (848 kg CO2-eq. t−1) and had highest C efficiency, C sustainability index and C efficiency ratio. Selection/development of high yielding and biotic (mainly, nematodes) and abiotic (mainly, Fe deficiency) stress tolerant varieties for direct seeded rice would help reduce/bridge the yield gap with puddled transplanted rice and further enhance crop and biomass yields and energy productivity of CA based rice-wheat cropping system.