When the Florentines conquered Pisa in 1406, the medieval walls were reinforced with the construction of a large quadrangular bulwark, the Old Citadel, in the vicinity of the bridge Ponte a Mare. This work probably also involved Filippo Brunelleschi whom we know was in Pisa in 1424 supervising the fortification of the tract of walls near the Porta a Lucca gate. A few years later, Pisa’s defensive system was further reinforced in 1440 with the realisation of a second stronghold, the New Citadel, sited on the opposite side of town. After the second conquest of Pisa in 1509, the project for the fortifications system was entrusted first to Antonio, and later to Giuliano da Sangallo. In 1512, the New Fortress was terminated, a large bastion towards the Arno that enlarged the "New Citadel". The structure was substantially not modified by Cosimo I who attended to strengthening the defensive layout with the construction of new bastions in the areas of the Porta Calcesana and Porta a Mare gates.

In the 18th century, the Garden inside the "New Citadel" hosted the meetings of the Colonia Alfea (the Pisan Arcadia): its illustrious guests included Carlo Goldoni who recited a sonnet there. In the early 19th century, the garden was transformed by architect Giovanni Caluri on behalf of Domenico Scotto, a shipping magnate from Livorno who purchased the property in 1798. The sculptural elements that adorned it once included the nineteenth-century statue of Pisan mathematician Leonardo Fibonacci which today has been returned to the monumental cemetery. It has been a public park since the 1930s.