Display omitted •Ex situ biogas upgrading to 96% CH4 is achieved in thermophilic up-flow reactors.•The totality of H2 and CO2 is converted to CH4 reaching 0.25 LCH4/LH2 CH4 yield.•Higher gas recirculation and diffusers’ pore size improved gas-liquid contact.•H2 selectively enhances hydrogenotrophic methanogens and syntrophic bacteria. This study evaluates the efficiency of four novel up-flow reactors for ex situ biogas upgrading converting externally provided CO2 and H2 to CH4, via hydrogenotrophic methanogenesis. The gases were injected through stainless steel diffusers combined with alumina ceramic sponge or through alumina ceramic membranes. Pore size, input gas loading and gas recirculation flow rate were modulated to optimize gas-liquid mass transfer, and thus methanation efficiency. Results showed that larger pore size diffusion devices achieved the best kinetics and output-gas quality converting all the injected H2 and CO2, up to 3.6L/LREACTOR·d H2 loading rate. Specifically, reactors’ CH4 content increased from 23 to 96% and the CH4 yield reached 0.25LCH4/LH2. High throughput 16S rRNA gene sequencing revealed predominance of bacteria belonging to Anaerobaculum genus and to uncultured order MBA08. Additionally, the massive increase of hydrogenotrophic methanogens, such as Methanothermobacter thermautotrophicus, and syntrophic bacteria demonstrates the selection-effect of H2 on community composition.