The effects of two dietary inclusion levels of chia seed (CHigh and CLow) on the FA profile and CLA isomers in cheese was evaluated. Dry matter and fat contents in cheese were higher (P < 0.05) in CHigh compared with control and CLow and the content of C18:0, C18:1n9c, total monounsaturated fatty acids, total polyunsaturated fatty acids increased (P < 0.05); total CLA content in CHigh cheese increased (P < 0.05) from 0.32% to 0.66%. Compared with control, saturated fatty acids (SFA) decreased (P < 0.05) by 3.4% with CHigh, due to a reduction of C14:0 and C16:0 in the cheese. The following CLA isomers were increased (P < 0.05) by CHigh: cis-9, trans-11; trans-7, cis-9; trans-11, cis-13 and trans-12, trans-14. Addition of chia seed at 5.5% DM in dairy goat diets can be used to increase the amount of bioactive FA, such as cis-9, trans-11 C18:2 in cheese.