Policies encouraging shifts towards more plant-based diets can lead to shortfalls in micronutrients typically present in animal products (B-vitamins, vitamin D, calcium, iodine, iron, selenium, zinc, and long-chain omega-3 fatty acids). We modelled the effect of fortifying foods with these critical micronutrients, with the aim of achieving nutrition and sustainability goals, using food consumption data from Dutch adults (19–30 years). Three dietary scenarios were optimized for nutritional adequacy and 2030 greenhouse gas emissions (GHGE-2030) targets, respectively, with the fewest deviations from the baseline diet: (i) the current diet (mainly vitamin A- and D-fortified margarine, iodized bread, and some calcium- and vitamin D-fortified dairy alternatives and iron- and vitamin B12-fortified meat alternatives); (ii) all plant-based alternatives fortified with critical micronutrients; and (iii) fortified bread and oils. Optimizing the current diet for nutrition and GHGE-2030 targets reduced animal-to-plant protein ratios from ~65:35, to 33:67 (women) and 20:80 (men), but required major increases in legumes and plant-based alternatives. When fortifying all plant-based alternatives and, subsequently, bread and oil, smaller dietary changes were needed to achieve nutrition and GHGE-2030 targets. Fortifying food products with critical micronutrients, ideally with complementary education on plant-based foods, can facilitate the transition to healthier and more sustainable diets.