A biogas upgrading system can include a multiple stage membrane system that is configured to remove oxygen so that the biogas is upgraded to have a higher concentration of methane, a pre-selected oxygen (O2) concentration (e.g. less than or equal to 0.2 mol %, etc.), and a pre-selected carbon dioxide (CO2) concentration (e.g. less than or equal to 5 mol %, etc.). The membrane system can be configured to reject O2 by utilizing a low CO2/O2 selectivity that is within a pre-determined range (e.g. less than 5 or less than 4.5). In some embodiments, the upgraded biogas that is output from the system can be entirely made up of methane, carbon dioxide, and oxygen. In other embodiments, the biogas can be almost entirely composed of these components along with a small amount of nitrogen and a trace amount (e.g. less than or equal to 0.2%-0.1%, etc.) of other components.