Saint Sofia Church was constructed on the site of several former churches, the earliest of which dates back to the 4th-century. During this time, Sofia was known as the ancient Roman city of Serdica. 

Over the centuries, a series of subsequent churches were built on the site of the original 4th-century church only to be destroyed by invading forces. Following each wave of destruction, a new church was erected in its place. The current church that exists today is believed to be the fifth iteration of a religious building at this location. 

The most recent Saint Sofia Church was constructed sometime during the middle of the 6th-century when Bulgaria was under the reign of Byzantine Emperor Justinian I.

During the 16th-century the church was converted into a mosque to serve the Muslim population under the rule of the Ottoman Empire. The former church would remain a mosque for about three centuries. The mosque was abandoned in the 19th-century during Russia’s liberation of Bulgaria and was later re-established as a church.  

Archaeologists who have excavated the surrounding area discovered that the church stands above the remains of an ancient necropolis. Today, many of the ruinous tombs have been carefully unearthed and are open for the public to explore. This archeological work has helped to reveal the extent of the former Roman city.

There are several levels below the church that reflect various eras throughout history, each supported by several informative display panels. The undercroft features mosaics from the floors of the previous churches, as well as some 50 tombs some of which contain traces of frescoes and other ancient artifacts. Sections of each level have been fitted with modern staircases and transparent flooring to reveal and protect the surfaces below.