Hythane, the blending of hydrogen (H2) and methane (CH4), is attracting attention as it could accelerate the H2 economy. H2 and CH4 can be extracted from organic material by fermentation and anaerobic digestion, respectively, but this alternative bio-hythane also contains carbon dioxide (CO2) that must be removed. This work addresses the use of Aprotic N‑Heterocyclic Anion-based ionic liquids (AHA-ILs) for bio-hythane upgrading. Three AHA-ILs ([P2228][2-CNPyr], [P2228][3-IPyra], and [P2228][4-BrIm]) were evaluated at process scale by conducting rate-based COSMO-based/Aspen Plus simulations of the upgrading processes. A wide range of operating conditions were screened by modifying key process variables such as the absorption pressure and the desorption temperature, and the bio-hythane composition. Energy and AHA-IL consumptions were analyzed together with variable operating cost (VOC). Energy demand and VOC were used to identify the Pareto optimal for each case study using a Python code. In addition, a detailed economic study was performed for the best three systems. The proposed processes are very versatile and are capable of handling bio-hythane of different compositions, being 10 %mol H2, 60 %mol CH4, and 30 %mol CO2 the most suitable for better process performance. For this case, the energy demand is about 0.51–0.56 kWh/Nm3 and VOC is about 1 cent. $/Nm3. The AHA-IL [P2228][3-IPyra] exhibited the best results for both variables. The energy requirement is in line with the minimum energy required for amine scrubbing technology, while VOC can be reduced by up to 17–48 % compared with electricity-intensive water scrubbing, pressure swing adsorption or membranes. Although higher investment is necessary, the assessed bio-hythane upgrading processes have the potential to operate around 0.1 $/Nm3, with VOC contributing about 8 % to the total cost.