The present work represents the first study focused on controlled hydrodynamic cavitation applied as gas transfer system to supply the methanogenic archaea with exogenous H2 and CO2. Starting from a generic mixed inoculum sampled from a thermophilic full-scale anaerobic digester, a bubble column bioreactor was coupled with a rotating hydrodynamic cavitator and fed with different H2/CO2 loading rates. Process efficiency and long-term effects on process stability and microbial population were evaluated. Gas sparging through the controlled hydrodynamic cavitation device is feasible under the operating conditions tested, resulting in almost 100% efficiency in H2 utilization and recording a CH4 volumetric content more than 99% in the gas leaving the reactor, without any gas recirculation from the headspace. The experimental trials lasted about 160 days and the behavior of the bioreactor showed a substantial stability over the time. Metagenomic and FISH analyses were carried out at the end of the experimental trials, revealing a remarkable increase of hydrogenotrophic methanogens species, related to the selection-effect of H2 on community composition. The findings provide previously unidentified insights into long-term effect on process stability and microbial community diversity in the biological hydrogenotrophic methanation process coupled with a gas–liquid mass transfer system based on controlled hydrodynamic cavitation technology. © 2023 Elsevier B.V.

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