The circulation trading routes and the characterization of the silver metal used in the European continent in the 15–17th centuries are historical issues that are still open. This study aimed to bring an insight into the silver processed within a chronological framework in the Portuguese territory, relating the analytical data with the known historical information. This investigation developed on 230 high silver coins from two important Portuguese coin collections was based mainly on surface particle-induced X-ray emission (PIXE) analysis, complemented with a few energy-dispersive X-ray fluorescence (EDXRF) analyses. The silver processed in different timelines was discriminated based on the variation of the impurity contents, namely Au and Bi. European silver with high Au and Hg and low Pb and Bi contents supplied the 15th century chronologies, being replaced at the dawn of the 16th century by a new metal entering the Portuguese capital. This new metal, with low Au and high Bi contents, was probably derived from European argentiferous copper ores. By the end of the 1500s, the Philippine chronologies reveal the newly discovered Potosí silver, identified for the first time based on PIXE minor and trace element surface contents, distinguishable from the European silver in use until 1578 in the Portuguese territory, by Au contents <100 ppm and very low Bi contents.