Though neglected and half ruined, the church survived until 1856, when it collapsed in a major earthquake. Up until 1866 there was an octagonal baptismal font next to the church, behind a marble column topped by a sphere.

After it was demolished in 1867, marble and other spolia were used to rebuild the Church of St. Titus and pave the square at the Three Arches, as well as being built into the entrance to what is now the courthouse. In respect for the remnants (perhaps the sacristy), the Muslims built the Fatih Sultan Mehmet Mosque or Hukniar (Imperial) Mosque.

The mosque was demolished in 1912 to make way for the first archaeological museum in Heraklion.