The process used to upgrade natural gas, biogas and refinery-off-gas directly influences the cost of producing the fuel and often requires complex separation strategies and operational systems to remove contaminants such as hydrogen sulfide (H₂S) and carbon dioxide (CO₂). Here we report a fluorinated metal–organic framework (MOF), AlFFIVE-1-Ni, that allows simultaneous and equally selective removal of CO₂ and H₂S from CH₄-rich streams in a single adsorption step. The simultaneous removal is possible for a wide range of H₂S and CO₂ compositions and concentrations of the gas feed. Pure component and mixed gas adsorption, single-crystal X-ray diffraction and molecular simulation studies were carried out to elucidate the mechanism governing the simultaneous adsorption of H₂S and CO₂. The results suggest that concurrent removal of CO₂ and H₂S is achieved via the integrated favourable sites for H₂S and CO₂ adsorption in a confined pore system. This approach offers the prospect of simplifying the complex schemes for removal of acid gases.