The Church of St Nicholas was constructed out of interchanging rows of stones and brickwork, and measures 15.80 by 15.50 metres (51.8 × 50.9 ft). Architecturally, it is a three-naved basilica church; the naves were formed by two rows of columns which ran along the length of the cella (or naos). It has three entrances, all from the west, and three apses in the easternmost part. The side apses are smaller than the one in the middle, which features an elaborate three-part window and additional decoration. The narthex and the four-stepped adobe synthronon (stone benches for the clergy) were added during the second period of construction in the 13th century. The synthronon fits inside the middle apse and includes a throne with railings in the middle.
The church had an adjacent bell tower, which was a separate rectangular structure that lay to the southwest of the church. Its walls were 4–4.50 metres (13–14.76 ft) long and around 1 metre (3.3 ft) thick. Architects Vasilka Gerasimova–Tomova and Violeta Pesheva believe that it reached 15–16 metres (49–52 ft) in height and that it was built in the 1210s under Bulgarian despot Alexius Slav (fl. 1208–1228), a largely independent medieval ruler of Melnik and the Rhodope Mountains..
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