Goat production in Chile is carried out by poor small-scale farmers in semi-arid to arid agricultural conditions. Milk and cheese are the main products obtained using artisanal, cultural and traditionally preserved methods where women and children are usually in charge of production. The products are directly consumed by the family or sold to by-passers at relatively high prices. The welfare of goats under these type of production systems is currently unknown and no appropriate validated operational welfare indicators are currently available. The incorporation of a welfare assessment system may increase milk yield and cheese production, and may provide added-value. We identified 48 welfare indicators in the peer-review literature. Only 40 of the initial welfare indicators were validated by goat production stakeholders (farmers, veterinarians, technician, welfare experts) using the European Food Safety Agency guidelines. Further on-farm validation was carried out to select only those indicators that were operational under the production systems. A final 37 operational welfare indicators were obtained. A welfare scoring system was developed from all the indicators and validated under normal production conditions. The use of these validated indicators and the welfare score is appropriate to Chilean goat production systems and may successfully increase the sustainability of goat milk production and goat farmers in Chile.