Biodiesel is a promising renewable fuel, which may help to limit our dependence on fossil fuels. However, the presence of contaminants in biodiesel can affect the Cu speciation of the Cu-SSZ-13 selective catalytic reduction (SCR) catalyst, resulting in its deactivation and decreased durability. In situ Cu K-edge X-ray absorption fine structure (XAFS) scanning during a temperature-programmed reduction in hydrogen (H-2-TPR) has been applied here for the analysis of Cu speciation in Cu-SSZ-13 catalysts aged using pure and contaminated biodiesel fuels. XAFS data were analyzed using the multivariate curve resolution alternating least-squares (MCR-ALS) method. While only reduction from Cu-II to Cu-I was observed at temperatures below 500 degrees C for the catalyst aged using pure biodiesel, a one-step reduction of Cu-II to Cu-0 at temperatures between 400 and 500 degrees C was found for the catalyst aged using P-doped biodiesel. The transformation of isolated CuII species to Cu-II clusters was suggested for the catalyst as a result of aging using P-doped biodiesel. The catalyst aged using S-doped biodiesel showed mainly the reduction of isolated Cu-II to Cu-I, which was inhibited as compared to that observed for the catalyst aged using pure biodiesel. The reduction of the catalyst aged using P+S-doped biodiesel led to the reduction of Cu-II to both Cu-I and Cu-0. The phosphorus was responsible for the formation of Cu-II clusters during aging of the catalyst using P+S-doped biodiesel. This study reveals that the presence of phosphorus in biofuels should be strictly regulated to avoid major changes in the Cu speciation of Cu-SSZ-13 catalysts.