This work is the first archaeometric investigation on copper and iron wastes from the Phoenician site of Motya (Sicily, Italy), dating back to the 8th to the 4th century BC. The samples were analyzed through micro-Raman Spectroscopy (μ-RS), Optical Microscopy (OM), Scanning Electron Microscope-Energy-Dispersive X-ray Spectroscopy (SEM-EDS), High-Resolution Field Emission Scanning Electron Microscopy (HR-FESEM), and Electron Micro-Probe Analysis (EMPA). Micro-Raman techinique permitted to identify both primary phases, for example, calchopyrite, and secondary products such as cuprite and copper thrihydroxychlorides in the Cu-slags and goethite in the Fe-slags. SEM and HR-FESEM imaging showed the occurrence of inhomogeneous microstructures in the Cu- and Fe-slags due to elements segregation, solidification, and corrosion. EMPA data revealed that the archaeometallurgical wastes from Motya can be differentiated on the basis of their chemical compositions. These preliminary results showed different typologies of by-products, such as base metals speiss, copper slags from smelting sulfide ore with matte, and iron smelting and smithing slags, suggesting different stages of copper and iron productions