The complementary feeding period is a critical stage for growth and development. Infants in developing countries and selected individuals in developed countries may benefit from micronutrient supplementation, but long-term effects are still poorly explored. We have some evidence, coming from observational studies, of the role of iron in the second semester of life for optimal brain development and functioning through early adulthood, but the advantage seems to be restricted to those infants who are effectively iron-deficient. For long-chain polyunsaturated fatty acids we have limited observations from randomized trials that they could promote the maturation of visual acuity in the short-term, without direct evidence linking supplementation during the complementary feeding period to later functional measurements. Probiotics and prebiotics, as well as other micronutrients, such as zinc, represent new promising areas of investigating effects on the immune system. The medium- and long-term effects need to be extensively explored, and any type of association recorded to check the safety of dietary supplements, considering their overconsumption, starting at early ages, in western countries.