In the present study, in situ lichens (Flavoparmelia caperata) were used to assess the deposition of atmospheric trace elements in the metropolitan area of Huancayo (Junín, Peru). In total, ten sampling sites were chosen and categorized as urban, peri-urban (rural-urban) and rural areas according to land use. In addition, samples were also collected from a non-contaminated area categorized as a control site. The concentrations of 16 trace elements were measured using an inductively coupled plasma mass spectrometer (ICP-MS) and examined by enrichment factor (EF), hierarchical cluster analysis (HCA), and principal component analysis (PCA). Twelve of the 16 trace elements in urban and peri-urban sites present concentration higher than those at the rural and control sites (p < 0.05). The EF results revealed significant enrichment (at least twice that of the control site) of Ba, Cr, Cd, Pb, Sb, V, and Zn at most sites. PCA and HCA showed that more elements were derived from vehicular sources and fewer from agricultural and natural sources.