Within the European circular economy roadmap, it is important for wastewater treatment plant (WWTPs) to recover energy and become energy-neutral or -positive. In the last few years, it has become increasingly interesting to boost energy recovery through the biogas upgrading. The aim of this work is to study a rapid hydrogenotrophic methanogenic culture enrichment strategy capable of limiting the organic degradation unbalance and allowing a fast start-up phase of the in situ biogas upgrading reactors, at pilot- or full-scale. The approach was tested with two, plus one control, laboratory-scale continuous stirred tank reactors filled with anaerobic sludge collected from a full-scale WWTP. The experimentation lasted 50 days and was divided into five phases: the anaerobic digestion start-up followed by four H2 injection phases (H2/CO2 ranging from 1:1 to 4:1 on molar basis). Despite a temporary slight increase in the total concentration of volatile fatty acids during phase II (2.56 gCH3COOH·L−1), and in phase III a mild pH increase (anyway, below 7.4) indicating the expected CO2 depletion, the strategy proposed was effective. In the last phase, in the biogas a methane content of about 80% was achieved, thus suggesting that the use of H2/CO2 above the stoichiometric value could further improve the biological biogas upgrading.