In the 14th century, what today is known as Villa Gamberia belonged to the Benedictine nuns of San Martino a Mensola. Matteo di Domenico Gamberelli, Antonio and Bernardo Rosselino`s predecessor, bought the estate at the end of the same century. In 1610 the villa belonged to Zanobi Lapi. The villa as it is today is the result of the renovation ordered by the Capponi family, who acquired it in 1718.

In the 19th century the villa underwent several transfers of property and experienced some periods of decadence. Princess Giovanna Ghykha, sister of the Queen of Serbia, bought it in 1896. The Princess owned the villa until 1925 and commissioned its renovation.

During World War II the villa was severely damaged and was then sold to the Vatican. Marcello and Nerina Marchi bought it in 1952 and, on the basis of some ancient documents, began a renovation work, which terminated six years later.