Intensive tillage operations, indiscriminate use of irrigation water, chemical fertilizers, and pesticides and crop biomass burning have made the conventional rice–wheat (RW) system highly energy-intensive and inefficient. In the recent past, portfolios of climate-smart agricultural practices (CSAP) have been promoted as a potential alternative to improve the energy efficiency in conventional RW system. Therefore, to evaluate the energy input–output relation, energy flow and economic efficiency in various combinations of crop management options, a 3-year (2014–2017) on-farm study was conducted at Karnal, India. Various portfolio of management practices; Sc1-Business as usual (BAU) or Conventional tillage (CT) without residue, Sc2-CT with residue, Sc3-Reduce tillage (RT) with residue + recommended dose of fertilizer (RDF), Sc4-RT/Zero tillage (ZT) with residue + RDF, Sc5-ZT with residue + RDF + GreenSeeker + Tensiometer, Sc6-Sc5 + Nutrient expert were investigated. Present study results revealed that net energy, energy use efficiency and energy productivity were 11–18, 31–51 and 29–53% higher under CSAP (mean of Sc4, Sc5 and Sc6) in RW system than Sc1, respectively. However, renewable and non-renewable energy inputs were 14 and 33% higher in Sc1 compared to CSAP (4028 and 49,547 MJ ha−1), respectively, it showed that BAU practices mostly dependents on non-renewable energy sources whereas CSAP dependents on renewable energy sources. Similarly, the adoption of CSAP improved the biomass yield, net farm income and economic efficiency by 6–9, 18–23 and 42–58%, respectively compared to Sc1. Overall, the adoption of CSAP could be a viable alternative for improving energy use efficiency, farm profitability and eco-efficiency in the RW system.