The Counts of Montedoglio, Goffredo d'Ildebrando's heirs to the throne, governed the village of Pieve Santo Stefano for a long time. They called the citizens to move to those areas through the concession of advantages and privileges. They built the town walls and a church inside them, since the parish the modern town took its name from is outside the town.

In the XIII century, the town was the target of the Guelfs' expansionistic aims, in particular of Florence and Perugia to the extent that the emperor Frederick II was obliged to put it under his protection.
The continuing incursions on the part of the citizens of Arezzo and of the Biturgensi abbots from Sansepolcro finally caused Pieve to submit to the Town of Arezzo in 1255. Nevertheless, the blatant lack of military protection against the incursions of the Florentines led the inhabitants of Pieve to call the Bishopric of Arezzo to help them. It became the free town's defence against the alliance between Sansepolcro and Perugia at the end of the century.
In the XIV century Pieve was characterized by the harsh war between Guelfs and Ghibellines. Paradoxically, the bishop of Arezzo, Guido Tarlati, belonged to the Ghibellines, since he was in disfavour with the Pope but he was supported by the emperor. In 1318, Tarlati occupied Pieve and made it the chief town of the viscountcy of the Val di Verona. A Guelph league contrasted its exuberance that also led him to conquer Cittą di Castello.
In 1337, the warrior-bishop was defeated and his territories were divided between Florence and Perugia. The latter, therefore, annexed Pieve. In 1359, after the inhabitants of Pieve rebelled, the town went back under Arezzo that was already dominated by the Florentine Republic. Pieve formally submitted to Florence in 1385 with the aim to avoid the battles between feudal lords definitively.
Thus, Pieve became the chief town of the town hall of the Val di Verona, that was included in the vicariate of Anghiari. With the arrival of the Medici a period of splendour started and interested Pieve, too, which was enlarged and enriched with Renaissance palaces, new walls and a fountain decorated with beautiful Della Robbia's ceramics set near the praetorial palace. The new castle was assaulted by the imperial troops of the Landsknechts in 1527, but it could resist the terrible collision of German armies by driving them back. In 1545, Pieve also became a vicariate's chief town.
Pieve's period of splendour was interrupted by the terrible plague that spread all over the Italian peninsula in the XVII century. In 1631, this mortal disease flagellated the area of Pieve. The inhabitants of the town, therefore, prayed the Madonna dei Lumi asking for a grace. They went to the sanctuary built in her honour in 1589. Its construction took place after the miraculous procession of angels paying homage an image of the Virgin Mary painted in the XV century that since then had become an object of worship and miracles. The plague prodigiously calmed down and since that time the town has been celebrating the birth of the Virgin Mary each 8 September.
In 1838, the vicariate of Pieve disappeared and was included by the one of San Sepolcro. In the following years, the restructuring works of the Collegiata were started so it could improve its appearance. In effect, the city had more than 4000 inhabitants. Unfortunately, one flood of the Arno in 1855 and a new epidemics of cholera menaced the wealth of the town. After the Grand Duke Leopoldo II escaped from Tuscany after the Risorgimento uprisings, Pieve Santo Stefano entered the newly born Kingdom of Italy in 1860.