The decline began on 6 August 1284, when the numerically superior fleet of Pisa, under the command of Albertino Morosini, was defeated by the brilliant tactics of the Genoese fleet, under the command of Benedetto Zaccaria and Oberto Doria, in the dramatic naval Battle of Meloria. This defeat ended the maritime power of Pisa and the town never fully recovered: in 1290 the Genoese destroyed forever the Porto Pisano (Pisa's Port), and covered with salt. The region around Pisa did not permit the city to recover from the loss of thousands of sailors from the Meloria, while Liguria guaranteed enough sailors to Genoa. Goods continued to be traded, albeit in reduced quantity, but the end came when the River Arno started to change course, preventing the galleys from reaching the city's port up the river. It seems also that nearby area became infested with malaria. Within 1324 also Sardinia was entirely lost in favour of the Aragonese.

Always Ghibelline, Pisa tried to build up its power in the course of the 14th century and even managed to defeat Florence in the Battle of Montecatini (1315), under the command of Uguccione della Faggiuola. Eventually, however, divided by internal struggles and weakened by the loss of its mercantile strength, Pisa was conquered by Florence in 1406. In 1409 Pisa was the seat of a council trying to set the question of the Great Schism. Furthermore in the 15th century, access to the sea became more and more difficult, as the port was silting up and was cut off from the sea. When in 1494 Charles VIII of France invaded the Italian states to claim the Kingdom of Naples, Pisa grabbed the opportunity to reclaim its independence as the Second Pisan Republic.

But the new freedom did not last long. After fifteen years of battles and sieges, Pisa was reconquered in 1509 by the Florentine troops led by Antonio da Filicaja, Averardo Salviati and Niccolò Capponi. Its role of major port of Tuscany went to Livorno. Pisa acquired a mainly, though secondary, cultural role spurred by the presence of the University of Pisa, created in 1343. Its decline is clearly shown by its population, which has remained almost constant since the Middle Ages.

Pisa was the birthplace of the important early physicist, Galileo Galilei. It's still the seat of an archbishopric; it has become a light industrial centre and a railway hub. It suffered repeated destruction during World War II.