The church of Saint Panteleimon in Nerezi near Skopje is a superb example of the Comnenian art on the all-Byzantine level. Commissioned by several members of the royal Comnenus family, the church was not finished until 1164. Nerezi is famous for its frescoes, representing a pinnacle of the 12th-century trend of intimacy and spirituality. They are often compared with similarly delicate works by Giotto, who worked 140 years later. These murals underwent serious 19th-century overpainting but were restored lately.

A Roman aqueduct survives to the north of the city. One of stone bridges connecting both side of Vardar River dates back to the reign of Stefan Dušan. This bridge is not to be confused with the more famous Stone Bridge in the city square built under the patronage of Sultan Mehmed III the Conqueror between 1451 and 1469, today featured as the amblem of the city of Skopje. Within Skopje, there are notable buildings from the Ottoman rule such as the Kuršumli Han (medieval Turkish inn) and several mosques.