In terms of architecture, three periods of construction can be identified in the now existing church. Its oldest (east) part is referred to the 10th-12th century and represents a small, almost square cross-domed church with a narthex to the west, traces of which are discernible to this day. The second period of construction was in the 13th century. In 1259 Sebastocrator Kaloyan, the local governor, undertook to rebuild the church. A two-storied structure was put up to the west of the church; the narthex was built anew and a small chapel was raised on top of it, which is thought to have been connected with the living quarters of the ruler. During the 19th century the church was extended again, whereby a new two-storied narthex was annexed to Kaloyan’s church, while the western wall was pulled down. In this way the three parts of the church, built in different periods, were arranged along a common axis lengthwise. One can get an idea of the original look of the 13th century church from the preserved frescoes, presenting a scale-model, carried by the church donor. The mural paintings in it are of different periods.

The extraordinary popularity of the Boyana Church is due to its 13th century mural paintings, which have been almost completely preserved from that time. It becomes clear from the donor’s inscription on the north wall of the narthex that the church murals had been painted during the reign of Tsar Konstantin Tih Assen in 1259. Of special interest are the characters of the donor – Sebastocrator Kaloyan - and his young wife Desislava, painted with a keen psychological insight. They can be seen on the eastern end of the north wall facing the patron St Nicholas, to whom Kaloyan is presenting a scale model of the church. Just opposite them are the likenesses of Tsar Konstantin Tih Assen and Queen Laskarina, depicted with no less feeling and skill. The inspired images of well-known monks and female saints are painted on the rest of the walls. Appearing here for the first time in art is the image of St Ivan Rilski [John of Rila] (9th-10th century) the saint and divine patron of the Bulgarian people. The moving beauty of the mural paintings is an eloquent proof of the skill of the anonymous mural painter, generally known as the Boyana Master Painter, showing alongside the established tradition a new, personal and different world outlook. What has been created in the Boyana Church marks a culmination in Bulgarian medieval mural painting and reveals to the world the achievements of the Bulgarian creative genius