The history of this pharamcy is closely linked to that of the Florentine Hospital of Santa Maria Nuova, to which it was annexed as "Spezieria". Here worked the "Speziale", officially a member of the hospital staff, responsible for preparing the remedies prescribed during medical examinations and supervising the professional training of young pupils. The medications were prepared from the medicinal herbs grown first in the Giardino dei Semplici in Via Sant'Egidio (no longer existing) and then in the Orto dei Semplici at San Marco (today's Botanical Gardens).

After a period of decline, the pharmacy was remodelled for the first time by Ferdinand I de' Medici, and again in 1789 by Peter Leopold of Lorraine. With the opening of the modern Careggi Hospital in 1934, the pharmacy's furnishings, manuscripts and ancient prescription books were divided among the Pharmaceutical Department of the Careggi Hospital, the Institute and Museum of the History of Science, and the Library of the University's Faculty of Medicine. Surviving today of the ancient pharmacy are rooms with coffered ceilings and the insignia of Saints Cosmos and Damian.