Biochar-amended soils have been explored to mitigate landfill methane (CH4) emissions. Recently, efforts have been made to mitigate other landfill gas (LFG) components such as carbon dioxide (CO2) gas and hydrogen sulfide (H2S) along with CH4. In this regard, a biogeochemical cover system is being proposed that incorporates biochar-amended soil and basic oxygen furnace (BOF) steel slag to simultaneously mitigate CH4, CO2 and H2S. In this study, long-term column incubation tests were performed to evaluate the gas mitigation potential of the biogeochemical cover system as well as investigate the effect of the BOF slag layer on microbial community composition and CH4 oxidation potential of the underlying biochar amended soil layer. The biogeochemical cover showed significant potential to remove CH4 and CO2 leading to zero emissions of CO2 into column headspace during incubation. Oxygen penetrated through the BOF slag layer into the biologic layers without affecting microbial activity and methane oxidation. Biochar-amended soil showed higher methane oxidation rates (46.2 µg CH4 g–1 day–1) than soil control (39.2 µg CH4 g−1 day−1) mainly in the upper 5 cm of the biologic layer. Methane oxidation rates decreased with depth in the biological layers in both columns. Both soil control and biochar-amended soil samples were dominated with methanotrophs such as Methylobacter, Methylocystis, Methylosinus, Crenothrix, and Methylomicrobium, across all the depths. Methylobacter genus, a Type I methanotroph, dominated the samples across all depths whereas showed decreasing abundance with depth. Biochar-amended soil had a greater abundance of methanotrophs mainly in the top 5 cm of the biologic layer consistent with the CH4 oxidation rate. Overall, biogeochemical cover soil performed relatively better than landfill cover soil alone in terms of CO2 sequestration, CH4 oxidation and microbial colonization making it a sustainable alternative for LFG management.