- The Church of the Holy Apostles was built by the Serbian Archbishop Arsenije in the 13th century and was painted in 1250. At the same time, the seat of the Serbian Church was also transferred to Pec.
- The Church of St Demetrios was built around 1320 by Archbishop Nikodim.
- The Church of the Virgin Hodegetria was built Archbishop Danilo II some time after 1320.
- The Church of St Nicholas was attached to the complex of churches at the same time as the Church of the Virgin Hodegetria was constructed.
The complex experienced difficult times during the early Turkish occupation. However, with the restoration of the Serbian Patriarchate of Pec in 1557, the place regained its focal spiritual and political role. In 1565 the narthex was painted and the iconostasis renovated, and frescoes were refreshed in 1620-21. During the time of Patriarch Pajsije, the church of the Holy Apostles was restored, and in 1633-34 the western part was repainted as the old frescoes have been seriously damaged. In the time of Patriarch Maksim, in 1673-74 the church of St. Nicholas was painted.
During the war between the Turks and Austrians the Serbs fought on the Christian side and the patriarchate was badly damaged. The monastery's treasury was transported to the Monastery of Gracanica and hidden in one of its domes; however, the Turkish rebel Jeghen Pasa discovered this location and removed the treasure in 1688. In 1690, ahead of the Turkish offensive spearheaded by Tatar and Albanian irregulars, Patriarch Arsenije III Carnojevic was forced to flee to safety in Belgrade. After the Turks took Belgrade in October of 1690, he withdrew to the Hungarian side with about 30,000 Serbian refugees. The Turks and Albanians plundered and desecrated the monastery, as well as many other Serbian sanctuaries. The Patriarchate was abandoned in another war with the Turks, 1737-1739, when Patriarch Arsenije IV Jovanovic and the monks left for Srem, taking with them the remaining valuables. Yet another demolition the monastery suffered by the Aslan Pasa of Bosnia in 1831.