Alternative protein sources (APSs) have emerged as a potentially healthy and, presumably, environmentally sustainable solution for meeting future food demand. Here we develop a new complex nutrient profile model to assess the nutritional quality of protein-rich foods, which, concurrently, allows to evaluate their environmental implications efficiently through the application of life cycle assessment (LCA). The development of the index was guided by the identification of priority nutrients in APSs and main deficiencies of similar models, which gave rise to the ‘quality Nutrient Rich Food 1.10.2’ (qNRF1.10.2). This model is the first nutrient profile system that combines various essential nutrients and a protein quality scoring system, namely Digestible Indispensable Amino Acid Score (DIAAS). From a nutritional perspective, its accuracy was proven and its application identified animal products as the most nutritionally complete food group, surpassing plant-based alternatives. However, when using the index as functional unit in LCA of protein-rich foods, we discovered that seeds, nuts, and mixtures of vegetable foods reported the lowest environmental impacts as a function of their nutrient density. Some exceptions were found for algae or insects, which performed worse than animal-derived foods in terms of resources consumption, or for cereals, which shown an important water deprivation potential. These results suggest that we should find a trade-off between the production of emerging and conventional foodstuffs, and that main environmental issues of each region should condition the location of production systems.