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.