School–museum partnerships have gained considerable attention in the academic literature in recent decades. However, their role in enhancing science education is still an under-researched topic. This work reports on the outcomes of the recovery, study, cataloging, and valorization of the 18th century geo-mineralogical collection belonging to the Collegio Nazareno, now housed at the Istituto San Giuseppe Calasanzio in Rome. The project, which was participated in by the students enrolled in the fourth- and fifth-grade high school classes, revealed rare specimens such as the mineralogical collection donated by the Holy Roman Emperor Joseph II (1741–1740) in 1785. Furthermore, the laboratory activities organized from the stored samples highlighted educational approaches that helped students to cope with the complexities of authentic scientific work and cultural related issues. This work thus offers significant insights into the importance of natural history school museums as useful (and oft-forgotten) learning tools in science education.