Pressure swing adsorption (PSA) is one of the industrial separation processes for biogas upgrading to produce biomethane. Biogas generated from biological feedstocks can have strong variations in composition and flow rate. To tackle these variations while maximizing the performance of a PSA process, an advanced control strategy should be developed. In order to develop an advanced control system that maximizes performance of the biogas upgrading PSA under the presence of severe feed disturbances, a perturbation analysis has been performed. Zeolite 13X was used as selective adsorbent for CH4–CO2 separation and binary breakthrough curves, and single-column PSA experiments were performed. Step-function perturbations of 5% in inlet flow rate and CO2 composition were introduced in the PSA. The PSA experiments have demonstrated that a change in flow rate or in CO2 composition leads to a variation less than 2% in the temperature at the top of the column. The gas composition, at the column outlet, in the adsorption step, increases as the position of the CO2 concentration front propagates further. This work shows that temperature variations inside the column can be used as observers to monitor the location of the CO2 concentration wave and, therefore, to be able to take decisions on the PSA step times. These observers (thermocouples) should be implemented in the top of column where the variation is more pronounced.