In this study, we investigated the lipid composition of fresh and semi-hard goat cheese produced in three Italian farms as well as the welfare assessment of goats reared in these farms. The fatty acid (FA) profile of cheese samples were found to be strictly related to the livestock system. Cheese collected from farms in which goats were allowed to graze and were fed diets with a higher forage/concentrate (F/C) ratio showed a FA profile represented by higher contents of health-promoting fatty acids. In the same samples, the health lipid indices showed the most favorable values. Conversely, cheese samples collected from a conventional-lowland farm, where goats were fed with higher amounts of concentrates and lower F/C ratio, presented a lower nutritional quality, characterized by the worst results for what concerns the health lipid indices. Then, we built a multivariate model able to discriminate samples coming from farms managed by a low-input system from those coming from farm managed by a high-input system. The comparison of animal welfare measurements and fatty acids data showed that a better intrinsic quality of low-input farms did not always correspond to better extrinsic quality, suggesting that the information on the livestock system is not always enough to provide consumers with complete awareness of the total product quality.