It originally comprised three aisles with two rows of marble columns, an apse and a narthex.

The Arabs maintained a garrison, using the structure as workshops, stables and living quarters for the army.

In 688 AD, after they evacuated the island, the church was restored as a three-aisled barrel vaulted basilica in a smaller scale than the previous one.

In the following years a smaller structure was built upon the ruins of the basilica but it was also destroyed by the 1222 earthquake.

Today, the Panagia Limeniotissa basilica is part of Paphos Archaeological Park which is a UNESCO World Heritage Site.