inand favoured the city because of their support, and exempted Pécs from paying taxes. Pécs was rebuilt and fortified.
In 1529 the Ottomans captured Pécs again, and went on a campaign against Vienna. The Ottomans made Pécs to accept King John (who was allied with them) as their ruler. John died in 1540. In 1541 the Ottomans occupied the castle of Buda, and ordered Isabella, the widow of John to give Pécs to them, since the city was of strategic importance. The citizens of Pécs defended the city against the Ottomans, and swore loyalty to Ferdinand. The emperor helped the city and defended it from further Ottoman attacks, but his advisers persuaded him into focusing more on the cities of Székesfehérvár and Esztergom instead of Pécs. Pécs was preparing for the siege, but a day before, Flemish and Walloon mercenaries fled from the city, and raided the nearby lands. The next day in June 1543 the Bishop himself went to the Ottomans with the keys of the city.
After occupying the city the Ottomans fortified it and turned it into a real Ottoman city. The Christian churches were turned into mosques; Turkish baths and minarets were built, Qur'an schools were founded, there was a bazaar in place of the market. For a hundred years the city was an island of peace in a land of war. She was a sanjak centre in Budin Eyalet at first and Kanije Eyalet later as "Peçuy".
In 1664 Croat nobleman Nicholas Zrínyi arrived in Pécs, with his army. Since the city was well into the Ottoman territories, they knew that even if the occupy it, they could not keep it for long, so they planned only to pillage it. They ravaged and burned the city but could not occupy the castle. Mediaeval Pécs was destroyed forever, except the wall encircling the historical city, a single bastion (Barbakán), the network of tunnels and catacombs beneath the city, parts of which are closed down, other parts are in possession of the famous Litke champagne factory, and can be visited
