The pressure global food systems exert on the environment has amplified over time, following the growth of the human population, changes in the food consumption patterns and intensification of the production systems. Without changes in food systems, an overpressure on agriculture and food production will be unavoidable, with inevitable consequences for the environment and human health. Animal‐derived protein production like meat and milk is among the most important drivers of this impact. Under this context, the evaluation of the health and sustainability impacts of alternatives for animal‐based food proteins are central aspects of this discussion. Health risk‐benefit assessment (RBA) of foods estimates the overall human health impact following exposure to a particular food or food component, integrating risks and benefits in comparable measures. Methods that simultaneously consider the environmental impact of the food production systems were needed to perform a sustainable holistic assessment. “ALTERNATIVA | Alternative protein sources in the European diets – integrating health risk‐benefit and sustainability” aimed to develop a holistic approach to assess the impact of alternative protein sources, integrating health and sustainability assessment. This project, considering five complementary work packages, developed activities to enhance the capacity‐building among members of the consortium in applying methodologies related to the health RBA and sustainability impact assessment; to develop, in collaboration with different stakeholders, a protocol to integrate the assessment of the impact of foods/diets on health and on sustainability; to apply the derived framework to a case study, to validate it with a real case scenario, estimating the health and sustainability impacts of replacing red meat consumption by pulses in two different countries; and to disseminate and promote the established method of integrated health and sustainability assessment to other potential EU users. This external scientific report summarizes the main outputs and results obtained in the context of the ALTERNATIVA project.