Vlatadon Monastery was a stauropegion, that is a monastery attached directly to the Ecumenical Patriarchate in Constantinople. It is now the only Byzantine monastery in Thessaloniki still functioning. It is one of the 15 Paleochristian and Byzantine Monuments of Thessaloniki that were included in the UNESCO World Heritage List in 1988.

The katholikon is now surrounded by the modern buildings of the Patriarchal Foundation of Patristic Studies founded in 1968. The monastery, dedicated originally to Christ Pantokrator, and is now dedicated to the Transfiguration. It was founded by Dorotheos Vlatis, when he was Metropolitan of Thessaloniki from 1351-71. While the dates are unclear, it is certain that it was taken over by the Ottomans at least for a short period of time. This can be seen in certain architectural features as well as the hammering of the frescoes to secure a better purchase for the plaster with which they were covered when it was converted into a mosque.

The importance and economic prosperity of the monastery, from its very foundation, are attested by the metochra it maintained both inside and outside the city, including the monydrion of Hagios Nikolaos Orphanos. 
The katholikon of the monastery is a relatively rare variation of the cross-in-square church, in which the dome is supported not on columns but on the walls of the sanctuary and on two pillars at the west. It has been demonstrated by recent investigations of the monument that this unusual feature was dictated by the existence of an earlier church on the same site, the remains of which still existed in the 14th century and determined the structure of the katholikon. During the course of these investigations, a number of tombs were discovered both inside and outside the katholikon, dating from the 14th to the early 16th century. 
The core of the church is enclosed by an ambulatory that ends at the east in two chapels. The north chapel and the north, west and part of the south ambulatory are from a later repair, in 1801. The open porticoes at the south and the west propylon are due to a repair of 1907. The church is constructed of masonry similar to that of the churches of Hagios Nikolaos Orphanos and the Taxiarches, with rows of stones alternating with pieces of brick. The eight-sided dome is brick-built, with brick half-columns at the ends of the sides, and six windows. The decorative brickwork is confined to the sanctuary apse. 
Work carried out in 1980-81 uncovered the wall-paintings of the nave and the east wall of the west ambulatory. The iconographic program includes Christ Pantokrator with the angelic powers and full-length prophets on the dome, all overpainted at a later period. On the intrados of the arches are preserved scenes from the Dodekaorton, and the walls have two zones of saints, mainly hermits and monks. In the ambulatory, there are military saints in the lower register, with scenes from the Miracles of Christ above them. The scenes of the Baptism and the 'Three Youths in the Fiery Furnace' in the two small apses in the narthex escaped the hammering received by the other wall-paintings. The paintings in the south chapel, which is dedicated to the Apostles Peter and Paul, have long been known, but can hardly be seen today because of the soot that has covered them. 
The wall-paintings are dated to between 1360 and 1380. The iconostasis probably belongs to the 17th century, though some parts of it, such as the parapet slabs, are 19th century repairs. The iconostasis in the north chapel was also constructed in the 19th century. The sacristy of the monastery contains a large number of very valuable icons, dating from the 12th to the 19th century.