The objective of this study was to determine the trace element composition and the toxic metal residues in Galician cow’s milk cheese produced in different systems (artisan, industrial, and organic). Fourteen elements (As, Cd, Co, Cr, Cu, Fe, Hg, I, Mn, Mo, Ni, Pb, Se, and Zn) were determined in 58 representative samples of Galician cheeses by inductively coupled plasma mass spectrometry. The toxic elements were present at low concentrations, similar to those reported for other unpolluted geographical areas. The essential elements were also within the normal range in cheeses. There were no statistically significant differences between smoked and unsmoked cheeses for any of the elements. Chemometric analyses (principal component analysis and cluster analysis) revealed that the industrial cheeses produced in Galicia using the milk from intensive dairy farms were different, in terms of elemental content, from artisan and organic cheeses, in which the elemental contents were similar.