The Certosa di Calci (Pisa) is one of the most important Carthusian monasteries in Italy. Its construction was authorised in 1366 and the first nucleus of the complex was completed by the end of the 14th century. During its long life, the Certosa underwent several transformations until it was abandoned by the monks in the 1970s. The Ministry of Culture took over its management with the creation of the National Museum of the Monumental Certosa of Calci. Later, part of the complex was ceded to Pisa University, who set up a Museum of Natural History there. In 2018, the MAPPA Laboratory at Pisa University began excavations whose principal aim was the analysis of the gardens associated with the cells of the prior, the apothecary and the ‘Padre Maestro’, intended as heavily anthropized ‘landscapes’ of limited dimensions, in order to study their formation and relationships with the wider surrounding environment, that is the vegetation and cultures both inside and outside the monastic building. For example, in the prior’s garden the excavations were able to explore the phases relating to the period preceding the building’s construction (14th century), the late 18th century restructuring and the abandonment in the late 20th century. Pollen analysis attests a great variety of plant species suggesting a garden continuously in flower, with ornamental flowers and plants such as roses, lilies and waterlilies, vegetables and medicinal species. The anthracological and carpological analyses attest the exploitation of timber resources from the Mediterranean macchia and the temperate deciduous forest for their fuel needs. It was also possible to define the agricultural practices and the cultivation of fruit trees such as chestnut, olive, almond and vines.