Although a large number of Spanish secondary schools have preserved an important scientific heritage, including large scientific instrument collections, this heritage has never been officially protected. Their current state is very diverse, and although several research projects have attempted to initiate their recovery and use, their lack of coordination and wide range of methodological approaches has limited their impact. This paper presents a case-study integrated in a new project supported by the Catalan Scientific Instrument Commission (COMIC) whose final aim is the establishment of a research hub for the preservation, study and use of Spanish scientific instrument collections. Major aims in this project are promoting a better coordination of Spanish projects in this field, and furthering international research on science pedagogy and the material culture of science. The major focus of COMIC is currently the recovery of secondary school collections. This paper provides first, a historical account of the development of secondary education in Spain, and the contemporary establishment of physics and chemistry school collections. Second, we focus on a case-study of three Spanish schools (Valencia, Castellon, and Alicante). Finally, we provide a brief overview of current projects to preserve Spanish school collections, and discuss how COMIC can contribute to help to coordinate them, and to take a step forward interdisciplinary research in this context.