Recent archaeological excavations have revealed that Giardino Scotto area (that has not always been a park) underwent many changes. Because it was alongside the main via Aemilia Scauri, road it was probably already partially inhabited in Roman times. It was abandoned completely throughout the early middle ages but in 1095 the church of S. Andrea in Chinzica was founded here. By the 13th century, it had become a thriving area of craftsmen, mostly potters, so it was known as Baractularia. During the 14th century several bell-foundries were set up for casting bells in bronze, a trade that the Pisan maestri excelled in.

After conquering Pisa in the 15th century, the Florentines built a fortified citadel here (1440-75), to keep watch on the inhabitants of the city. Brunelleschi took part in the project. In order to construct the citadel, all the constructions in the area were demolished but part of the medieval walls of the city were used, of which two semicircular towers and a stone wall and escarpment to the west still stand.

In 1495 the fortress was partly destroyed during a Pisan uprising. Between 1509 and 1512, following the second Florentine conquest, Antonio da Sangallo used part of the earlier construction to build a new star-shaped fort to the south, still visible today from piazza Guerrazzi, and a bastion on the banks of the Arno.

The fortress was dismantled in 1785 and in place of the bastion, a mansion was built, the property of Domenico Scotto, from whom it took its name. The part of the fortress behind the house became a private garden. In 1936, when the palazzo became the Regia Questura, the last heirs donated the park to the citizens of Pisa.