Based on FDA guidelines, heavy metals in APIs have to be controlled to stringent low levels (parts per million). Accordingly, a key part in process development is the removal of residual heavy metals from reaction streams. This presents a particular challenge when metal catalysts are used in the final API synthetic step. In this case, the final step in the preparation of an early drug candidate included the use of Pd as well as multiple Zn reagents. The synthetic route for the step produced high levels of palladium and zinc impurities which needed to be reduced to ≤ 10 ppm and ≤ 25 ppm, respectively, in the final API product. An extensive screening of single and mixed systems of metals scavengers was conducted to facilitate the efficient removal of both metals. In the end a single functionalized silica based scavenger was identified to be the most effective to achieve the necessary levels. The challenges encountered during the development of a scaleable process for this complex system will be discussed.