Human milk is a complex and dynamic biological fluid. Besides the basic provision of nutrition, it contains a wide range of bioactive molecules that support the immune and cognitive development of the infant, as well as their metabolic processes. Understanding the chemical diversity of human milk and quantifying how it differs from common artificial substitutes is thus central to the improvement of infant nutrition. In this work, a chemoinformatic approach has been adopted to characterize and compare the chemical spaces pertaining to human, bovine, and plant-based (i.e. soy) milks, as well as selected weaning foods. This was subsequently complemented with compounds with known bioactivity from curated molecular datasets, collected through a comprehensive review of the scientific literature and from specialized databases, including FooDB, MilkyBase, and PubChem.