Egg incubation waste in association with sheep manure might be an interesting alternative for improving energy efficiency in anaerobic co-digestion systems. The goal of this study was to determine whether the inclusion of liquid hatchery waste (LHW) can improve the energy efficiency of anaerobic digestion from sheep manure and whether this inclusion is economically viable. The study was carried out in a completely randomized 4 × 3 factorial design that corresponded to four LHW levels (0, 10, 20, and 30% total solids in the affluent) and three hydraulic retention times (HRTs; 12, 17, and 22 d). Greater reductions in chemical oxygen demand (COD, 58.00 and 60.59%) and volatile solids (VS, 75.91 and 79.44%) were attained with the inclusion of 12.65 to 14.43% at 17 and 22 d of HRT, respectively. The HTRs of 17 and 22 d presented similar biogas production; however, the HTR of 17 d led to higher concentrations of methane in the biogas composition (64.0%) compared to that at 22 d (62.2%). Using the ideal level of LHW and 17 d of HRT attained an increase in methane production by 25.36% compared with that of the isolated digestion of sheep manure. An economic viability analysis showed that the investment risk was low with zero probability of negative net present value (NPV). We concluded that co-digestion between LHW and sheep manure might improve energy generation and promote the economic sustainability of such energy production. Display omitted •Liquid hatchery residue generates clear energy.•Semi-continuous co-digestion is efficient in treating hatchery residues.•Adding lipid-rich residues enhances biogas and methane productions.•The inclusion of 13% liquid residue resulted in maximum methane production.•17 days are enough to break down the liquid hatchery residues.