Producción Científica Biogas contain minor concentration of volatile methyl siloxanes (VMS), responsible for severe damages in turbines or internal combustion engines. Sustainable biological processes for VMS abatement are limited by the low aqueous solubility of VMS. In order this limitation, the siloxanes (D4, D5, L2 and L3) removal performance of a two-phase partitioning biotrickling filter (TP-BTF) was study in terms of the empty bed residence time (EBRT) and the fraction of the organic phase (silicone oil). A decrease in the total VMS removal from 76 to 49% was observed when the EBRT was reduced from 60 to 15 min. The highest removals were achieved for D4 (53–84%) and D5 (69–87%), compared to the lower values recorded for L2 (19–45%) and L3 (31–81%). The increase in the share of silicone oil in the recycling mineral medium from 5 to 45% resulted in an improvement of the total VMS abatement from 35 to 52%. This enhancement was observed for L3 (21–50%), D4 (26–64%) and D5 (58–78%), whereas L2 removals remained < 25%. A highly specialized bacterial community dominated by the genus KCM-B-112 was retrieved at the end of the experiment. Bio Based Industries Joint Undertaking (Horizon 2020 grant 745785) Junta de Castilla y León (grants CLU 2017-09 and UIC 071) European Commission-H2020-MSCA–IF–2019 (project 897284)