This study evaluated the process performance and determined the microbial community structure of two lab-scale thermophilic trickling biofilter reactors used for biological methanation of hydrogen and carbon-dioxide for a total period of 94 days. Stable and robust operation was achieved by means of a single-pass gas flow. The quality of the output gas (>97%) was comparable to the methane purity achieved by commercial biogas upgrading systems fulfilling the specifications to be used as substitute to natural gas. The reactors' methane productivity reached >1.7 LCH4/(LR·d) at hydrogen loading rate of 7.2 LH2/(LR·d). The spatial distribution of the microbial consortia localized in the liquid media and biofilm enabled us to gain a deeper understanding on how the microbiome is structured inside the trickling biofilter. Sequencing results revealed a significant predominance of Methanothermobacter sp. in the biofilm. Unknown members of the class Clostridia were highly abundant in biofilm and liquid media, while acetate utilising bacteria predominated in liquid samples.