For renewable fuels to displace petroleum, they must be compatible with emissions control devices. Pure biodiesel contains up to 5 ppm Na + K and 5 ppm Ca + Mg metals, which have the potential to degrade diesel emissions control systems. This study aims to address these concerns, identify deactivation mechanisms, and determine if a lower limit is needed. Accelerated aging of a production exhaust system was conducted on an engine test stand over 1001 h using 20% biodiesel blended into ultra-low sulfur diesel (B20) doped with 14 ppm Na. This Na level is equivalent to exposure to Na at the uppermost expected B100 value in a B20 blend for the system full-useful life. During the study, NOx emissions exceeded the engine certification limit of 0.33 g/bhp-hr before the 435,000-mile requirement. Replacing aged diesel oxidation catalyst (DOC), diesel particulate filter (DPF), and selective catalytic reduction (SCR) devices with new degreened parts showed that each device contributed equally to the NOx increase. Following this systems-based evaluation, a detailed investigation of the individual components was completed. Na was determined to have minimal impact on DOC activity. For this system, it is estimated that B20-Na resulted in 50% more ash into the DPF. However, the Na did not diffuse into the cordierite DPF nor degrade its mechanical properties. The SCR degradation was found to be caused by a small amount of precious group metals (PGM) contamination that increased NH3 oxidation, and lowered NOx reduction. Therefore, it was determined that the primary effect of Na in this study is through increased ash in the DPF rather than deactivation of the catalytic activity.