This study was carried out within the project “Roma Hispana. Nuevas tecnologías aplicadas al estudio histórico, la musealización y la puesta en valor de Patrimonio Cultural español en Roma: la spezieria di Santa Maria della Scala” (Universitat de València Spain), which is funded by the Conselleria d’Innovació, Universitats, Ciència i Societat Digital of the Generalitat Valenciana (2020–2021) and authorized by the Sovrintendenza Speciale Archeologia Belle Arti e Paesaggio (Special Superintendence of Archeology, Fine Arts and Landscape) of Rome, Italy. The spezieria di Santa Maria della Scala was the oldest apothecary in Europe managed by the order of Discalced Carmelite friars. Operating between the second half of the seventeenth century and the mid-twentieth century, over time it acquired great prestige, becoming known as the Pharmacy of the Popes. The aims of the “Roma Hispana” project are to study, musealize and disseminate the material and immaterial cultural heritage of this historical spezieria by combining physicochemical and cultural studies, new 3D technologies, and artificial intelligence. As a case study, in this paper we report the application of a laser scanner prototype for 3D color imaging of the spezieria’s sales room and use a simpler photogrammetry method to collect analogous data in the small nearby storeroom coupled to the high-power capabilities of the ENEA parallel computer facility. Digital data were collected to enable a virtual tour that provides a fully navigable, faithful, high-resolution 3D color model to render this ancient Roman apothecary accessible and usable to interested members of the public and experts in the sector (art historians, restorers, etc.). We also describe the 3D technology used to obtain three-dimensional images of the cultural assets of these spaces (mostly drug containers) and its results. The ultimate aim of this study is to achieve the virtual musealization of the heritage complex.