He moved to Pisa in 1544, while maintaining his home in Bologna. He created the first herbarium (hortus siccus) in that year, drying plants while pressing them between pieces of paper, then gluing them to cardboard. 1544 also saw the establishment of a garden for live plants, which became known as the Orto botanico di Pisa.
Ghini published no significant botanical work of his own, but was noted as a teacher many of whose students went on to significant careers, including Cesalpino and Mattioli, the latter of which he helped by travelling around the Mediterranean and Near East looking for plants that matched the mystifying descriptions of Dioscorides. A Placiti describing Ghini's travels was published posthumously.