The Medicean Villa is located in Camugliano, a feudal centre at three kilometres from Ponsacco's downtown. It dates to the XVI century and it represents an indelible trace of the Medici's domination over the Pisan country for more than two centuries.

One villa near Camugliano was signalled in an act through which the Lucca's bishop Guido ceded it to a man called Teudegrimo, son of Farolfo, along with other goods in 980. In the Middle Ages, the village underwent numerous devastations by Florence and the Visconti's Milan troops in 1345.
Only with the arrival of the Medici the area started thriving, also thanks to the reclamations of marshes carried out by Matteo Botti at the end of the XVI century. It is in the upper part of his estate that the villa rises.
The construction works of the complex had been started in 1533 by Alessandro de' Medici, but they were finished by the Grand Duke Cosimo I.
A peculiar characteristic of the villa is the fusion of elements typical of the holiday resorts of that period with military elements. In effect, the complex has a quadrangular layout and it is surmounted by towers. The structures adjacent to it were conceived as stables and barracks.
This particular appearance was useful to the Medici when the insurrections of Pisa and the towns in Valdarno occurred in 1494 and 1530. Successively, the villa was given to Giuliano Gondi as a reward for his loyalty to the Medici and it was bought by Matteo Botti in 1568. The latter transformed the surrounding area into an agricultural estate.
In 1620, the villa returned into the Medici's hands until the institution of the Marquisate of Camugliano and Ponsacco, when the building and the territories of the Ponsacco city-state were granted to the nobleman Filippo Niccolini, whose family dominated over the area until 1781.