The effects of adding flaxseed or fish oil to the diet of dairy cows on the chemical and physical profile of Mozzarella cheese production were studied. The experiment involved 24 Friesian cows, divided into 3 groups accordingly fat supplementation: basal diet (CT), diet supplemented with flaxseed (FS) or fish oil (FO). Mozzarella cheeses were manufactured from bulk milk of each group. Bulk milk was analysed for chemical composition and renneting parameters. Mozzarella cheeses were analysed for chemical composition, fatty acid profile, and textural properties. Results suggest that Mozzarella cheese from cows receiving flaxseed supplementation showed a decrease in saturated fatty acids (SFA), an increase in monounsaturated fatty acids (MUFA), and in polyunsaturated fatty acids (PUFA) compared with control Mozzarella cheese. The increased dietary intake of C18:3 in flaxseed supplemented cows resulted in increased levels of trans-11 C18:1, and of CLA cis-9 trans-11 C18:2, and in low Atherogenic and Trombogenic Indexes. FO Mozzarella cheese showed compositional and textural properties quite similar to CT Mozzarella cheese; however, increased levels of n-3 polyunsaturated fatty acids in FO Mozzarella were found.