The present paper reports one of the first studies on the identification of natural resins and balsams in modern era drug formulations. Gas chromatography coupled with mass spectrometry (GC-MS) was applied to investigate the composition of ancient remedies and pharmaceutical formulations coming from the Spezieria di Santa Maria della Scala in Rome, founded at the end of the seventeenth century by the Discalced Carmelites. The obtained results highlight the presence of complex mixtures containing resinaceous and lipidic-based compounds. Thanks to the detection of characteristic markers, it was possible to identify several natural resins, such as guaiacum resin, ladano resin and scammony resin. Balsamic and aromatic compounds characteristic of essential oils were identified as well. In addition, an anti-inflammatory ointment, composed by mixing Venetian turpentine, a Pinaceae resin and a triterpene resin exudate of a plant from South America, was found among the analysed formulations. Combining the analytical results, the historical research and the botanical composition, it was possible to formulate compositional hypotheses of this historical medicine and provided some indications about their use in health. The study of historical drugs is not only important to know the practices handed down by apothecaries in the past, but also fundamental to reconstruct historical recipes that can inspire new dermatological, cosmetic, hygienic and current curative products.