Iron, zinc, and calcium are essential micronutrients that play vital biological roles to maintain human health. Thus, their deficiencies are a public health concern worldwide. Mitigation of these deficiencies involves micronutrient fortification of staple foods, a strategy that can alter the physical and sensory properties of foods. Peptide–mineral complexes have been identified as promising alternatives for mineral-fortified functional foods or mineral supplements. This review outlines some of the methods used in the determination of the mineral chelating activities of food protein-derived peptides and the approaches for the preparation, purification and identification of mineral-binding peptides. The structure–activity relationship of mineral-binding peptides and the potential use of peptide–mineral complexes as functional food ingredients to mitigate micronutrient deficiency are discussed in relation to their chemical interactions, solubility, gastrointestinal digestion, absorption, and bioavailability. Finally, insights on the current challenges and future research directions in this area are provided.