Following the union of Crete with Greece, the church was turned into a covered market. The central nave was converted into an arcade and the side ones became shops, with doors closing off the semicircular arches.

The only survivng features of the church are the lancet windows in the east wall, five further windows in the upper section of the side walls and two decorative rosettes crowning the outside of the east and west walls. At the bottom of one of the dividing arches in the north nave there was also a pillar hewn from a single block, bearing an inscription dating to the late 11^th or early 12 century. This derives from the earlier Byzantine church on the site, and was uncovered during excavations carried out after the Madonnina was demolished.