The objective of this study was to determine productive performance, milk composition and milk fatty acids (FA) of goats supplemented with sunflower and linseed whole seeds in grass silage‐based diets. Nine Alpine goats were grouped in a replicated 3 × 3 Latin square design (n = 3), that included three 21‐d periods. Treatments were based on grass silage offered ad libitum and a concentrate mixture supplemented with either 40 g/d of Megalac‐R® (control), 80 g/d of sunflower seed (SF), or 80 g/d of linseed (LS). Dry matter intake (1292 ± 14.0 g/d) and digestibility (g/kg) of dry matter (640 ± 32.1), organic matter (668 ± 32.4), neutral detergent fiber (628 ± 41.4) and acid detergent fiber (567 ± 60.9) was not affected by treatments (p >0.05). Treatment did not affect milk fat yield (39.9 ± 1.24 g/d), protein content (4.5 ± 0.03 %) and protein yield (34.7 ± 1.22 g/d). Compared to control, SF and LS, decreased C16:0 (28.2 vs. 23.1 and 22.4 g/100 g), and increased total C18:1 (24.1 vs. 27.6 and 28.4 g/100 g) respectively. Overall, SF and LS resulted an effective strategy for altering the FA composition of goat´s milk towards a healthier profile for humans without deleterious effects on animal performance.