The university system has always been based on the residential nature of the academic community. Those who wished to continue their studies and obtain an academic qualification had to enroll in a university, physically participate in lectures and laboratories, take exams and complete internships. This has resulted in significant migration flows among university students. Despite progress in methodologies and technologies for distance learning, STEM (Science, Technology, Engineering and Mathematics) disciplines continue to represent a critical challenge, especially due to the difficulty of effectively transferring laboratory exercises to an e-learning platform. This paper presents MetaLAM, an innovative virtual laboratory for teaching fundamental concepts in the multi-element chemical analysis of agri-food products, with particular focus on tomatoes, within the metaverse. Overcoming the limitations of traditional online and remote laboratories, MetaLAM offers an immersive 3D environment where students interact with “digital twins” of real laboratory instruments, for a dynamic and realistic learning experience. Digitally reproduced instruments include freezing dryers, analytical balances, digestion systems and inductively coupled plasma mass spectrometers (ICP-MS), which users can use to faithfully reproduce preparatory steps, strong acid mineralization and analysis of element concentrations in a tomato sample. The laboratory offers flexible access, which allows both synchronous and asynchronous learning, favoring the personalization of study times and increasing individual time with laboratory equipment, normally limited in traditional laboratories.