A field experiment was conducted for two consecutive years with the aim to quantify the role of different nutrient management variables such as microbial inoculation, zinc (Zn) fertilization and optimal and sub-optimal fertilization of nitrogen and phosphorus on the energetic and nutritional status of the rice–wheat cropping system (RWCS). The said nutrient management variables were applied over six different crop establishment methods (CEMs) in RWCS viz. puddled transplanted rice (PTR), system of rice intensification (SRI) and aerobic rice system (ARS) in rice and conventional drill-sown wheat (CDW), system of wheat intensification (SWI) and zero-tillage wheat (ZTW) in wheat. Two microbial consortia viz. Anabaena sp. (CR1) + Providencia sp. (PR3) consortia (MC1) and Anabaena-Pseudomonas biofilmed formulations (MC2) were used in this study, while recommended dose of nitrogen (N) and phosphorus (P) (RDN) (120 kg N ha−1 and 25.8 kg P ha−1), 75% RDN and Zn fertilization (soil applied 5 kg Zn ha−1 through zinc sulphate heptahydrate) were the other variables. The contribution of microbial consortia, Zn fertilization and RDN (over 75% RDN) to net energy production of RWCS was 12.9–16.1 × 103 MJ ha−1, 10.1–11.0 × 103 MJ ha−1 and 11.7–15.3 × 103 MJ ha−1. Among the CEMs, the highest gross and net energy production was recorded in ARS–ZTW with lowest energy required for production of one tonne of system yield (2366–2523 MJ). The system protein yield varies from 494.1 to 957.7 kg ha−1 with highest protein yield in 75% RDN + MC2 + Zn applied ARS–ZTW. Among micronutrients, the uptake of Zn and iron (Fe) is sensitive to all studied variables, while manganese (Mn) and cupper (Cu) uptake was found significantly affected by CEMs alone. The combination of 75% RDN + MC2 + Zn in ARS–ZTW was found superior in all respects with 288.3 and 286.9 MJ ha−1 net energy production and 2320 and 2473 MJ energy required for production of one tonne system yield in the first and second year of study, respectively.