Expressing the environmental impact of foods in relation to the nutritional quality is a promising approach in the search for methods integrating interdisciplinary sustainability perspectives. However, the lack of standardized methods regarding how to include nutrient metrics can lead to unharmonized results difficult to interpret. We evaluated nutrient density indexes by systematically assessing the role of methodological variables with the purpose of identifying the index able to rank foods with the highest coherence with the Swedish dietary guidelines. Among 45 variants of the nutrient density index NRF (Nutrient Rich Food), a Sweden-tailored NRF11.3 index, including 11 desirable nutrients and 3 undesirable nutrients, calculated per portion size or 100 kcal with the application of weighting, ranked foods most coherently with the guidelines. This index is suggested to be suitable as complementary functional unit (FU) in comparative life cycle assessment (LCA) studies across food categories. The results clarify implications of methodological choices when calculating nutrient density of foods and offer guidance to LCA researchers on which nutrition metric to use when integrating nutritional aspects in food LCA.