This study aimed to describe the underlying process, used methods and major recommendations emerging from a comprehensive and prospective health impact assessment of the endorsement of a front-of-pack nutrition labelling (FOP-NL) system by the Portuguese health authorities. A mixed-methods approach was used to gather information on the impact of four FOP-NL schemes on consumers’ selection of food products according to the perception of their nutritional quality, combining a systematic literature review, focus groups (FG), in-depth individual interviews, and an open-label crossover randomized controlled study. The relevance of FOP-NL as a public health promotion policy has emerged as a consensual idea among either FGs’ participants (i.e., consumers and experts), or interviewed stakeholders. Although all of the evaluated FOP-NLs result better than no system on promoting the choice of the healthiest product, the effectiveness of easy-to-interpret FOP-NL among vulnerable groups raised concerns related to the need of integrating specific nutritional information to promote a better self-management of chronic diseases, and related to the level of literacy of consumers, which could impair the usage of FOP-NL. Educational campaigns addressing skills to use FOP-NL is recommended. Furthermore, a monitoring strategy should be considered to evaluate the long-term effectiveness of this policy in promoting healthier food choices, and in reducing diet-related non-communicable diseases burden.