This paper illustrates an interdisciplinary educational experience aimed at transforming the study of biomolecules into active scientific investigation. Through the Inquiry-Based Learning (IBL) methodology, students explored the nature of cow’s milk not only as a food, but as an extraordinarily complex chemical-physical system. The program integrates the study of colloidal systems with experimental protocols for the separation and characterization of milk’s main components (caseins, whey proteins, lactose, and mineral salts). Particular attention was paid to lactose intolerance, as a health issue, and to the laboratory production of lactose-free milk. Furthermore, the valorization of dairy waste from a circular economy perspective was explored, with a focus on its reuse for the production of bioplastics, textile fibers, adhesives, and artistic applications. The activity allowed students to connect abstract theoretical knowledge to everyday phenomena, promoting scientific citizenship skills in line with the goals of the 2030 Agenda.