Conventional agriculture is energy and carbon intensive. Single and double-crop basis residue-mulching in zero-tilled crop-sequences may minimize carbon-footprint with improved crop and energy productivity in water-scarce ecologies. Zn-fertilization is also vital for drought-stress tolerance besides enhanced productivity and quality in Zn-deficient arid-soils. Hence, we compared the single and double-crop basis residue-mulching alongwith Hydrogel and Zn-fertilization in zero-tilled pigeonpea-wheat system. Results showed that double-crop residue-mulching + Hydrogel exhibited ∼22.3 and 17.1% higher system-productivity over no-residue and single-crop residue-mulching plots while maintaining higher net-returns (1315 US$/ha). Crop-residue covering consumed considerable energy (77.3–89.1% of total consumption) and carbon (5–10 folds). Thick residue-cover (8 t/ha/year) under double-crop residue-mulching + Hydrogel exhibited significantly higher energy-output (238,328 MJ ha−1), energy-intensiveness (107.3 MJ/US$) and specific energy (20.15 MJ kg−1) compared to single-crop residue-mulching; whereas energy-use efficiency, energy productivity and profitability were higher under no-residue cover. Zn-fertilization (5 kg ha−1) alongwith Zn-solubilizer in both crops also enhanced the biomass and energy productivity over sole-Zn or no-Zn. Interestingly, carbon footprints increased with residue-covering (4–8 t/ha/year) while least under no-residues. Therefore, farmers should preserve a balance while mulching the residues in single or both crops besides necessitating Zn-fertilization in Zn-deficient arid and semi-arid regions where livestock equally competes for residues as quality fodder. •Higher yield, energy output and profits in double-crop residue mulching in zero-tilled (ZT) sequence.•Zn plus Zn-solubilizer enhanced yield, profits and energy-use over sole use or no-Zn.•Crop residue covering consumed higher energy and carbon input and production costs.•Single-crop residue mulching more carbon and energy-use efficient over double-crop mulched plots.•Higher energy and carbon use efficiency in no-residue plots in ZT system.