The Boyana Church was built in three stages: in the late 10th and early 11th, the mid-13th, and the mid-19th centuries.

The oldest section (the eastern church) is a small one-apse cross-vaulted church with inbuilt cruciform supports. It was built in the late 10th and early 11th century.

The second section, which adjoins the eastern church, was commissioned by Sebastocrator Kaloyan and his wife Dessislava and in the mid-13th century. This building belongs to the two-floor tomb-church type. It consists of a ground-floor family sepulchre with a semi-cylindrical vault and two arcosolia on the north and south walls, and an upper-floor family chapel identical in design to the eastern church. The exterior is decorated with ceramic ornaments.

The last section was built on donations from the local community in the mid-19th century.