To date, information concerning pre-Colonial metallurgy in South America has largely been limited to the archaeological record of artifacts. Here, we reconstruct a millennium of smelting activity in the Peruvian Andes using the lake-sediment stratigraphy of atmospherically derived metals (Pb, Zn, Cu, Ag, Sb, Bi, and Ti) and lead isotopic ratios (206Pb/ 207Pb) associated with smelting from the Morococha mining region in the central Peruvian Andes. The earliest evidence for metallurgy occurs ca. 1000 A.D., coinciding with the fall of the Wari Empire and decentralization of local populations. Smelting during this interval appears to have been aimed at copper and copper alloys, because of large increases in Zn and Cu relative to Pb. A subsequent switch to silver metallurgy under Inca control (ca. 1450 to conquest, 1533 A.D.) is indicated by increases in Pb, Sb, and Bi, a conclusion supported by further increases of these metals during Colonial mining, which targeted silver extraction. Rapid development of the central Andes during the 20th century raised metal burdens by an order of magnitude above previous levels. Our results represent the first evidence for pre-Colonial smelting in the central Peruvian Andes, and corroborate the sensitivity of lake sediments to pre-Colonial metallurgical activity suggested by earlier findings from Bolivia.