The aim of this study was to evaluate the fatty acid profile and trace element content in three different Galician cow's milk cheeses (organic made from pasteurized milk, industrial made from pasteurized milk and artisanal made with raw milk). Twenty-five fatty acids and thirteen elements were determined by respectively gas liquid chromatography and inductively coupled plasma mass spectrometry, in thirty representative samples of the cheeses. The organic cheeses had significantly lower palmitic acid contents and significantly higher contents of odd and branched fatty acids, oleic acid, vaccenic acid, α-linolenic acid and conjugated linoleic acid than the other cheeses. The organic cheeses also had lower concentrations of trace and toxic element residues. Moreover, an association between medium chain fatty acids and palmitic acid and the presence of several mineral elements was detected by chemometric techniques. The nutritional evaluation of the organic cheeses was more favorable than for the other cheeses, as confirmed by the values of health-related indices.