Welfare assessment can play multiple roles in the path to welfare improvement. In the dairy goat area, identification of the main welfare problems across countries and different production systems is needed. By the application of a prototype welfare assessment protocol, based on animal-based indicators, we aimed to provide an insight into the main welfare problems affecting intensively kept dairy goats in Portugal. Thirty farms, organised in three size categories, were assessed. The main areas of concern were claw overgrowth, queuing at feeding and hindquarter dirtiness, with larger farms heading higher concerns. Additionally, this paper aimed to investigate indicators’ consistency over time. Ten of the 30 farms were revisited four months later, during which no major husbandry changes were made. Our results showed an overall consistency. This study can help define intervention thresholds or minimum legal levels for each indicator, by determining their overall prevalence.