The magnificent whitewashed structure actually consists of five churches built between the 15th and the 17th century. Four churches comprise the base – the church of Agios Efstathios in the centre, surrounded by the churches of Agios Anargyros, Agios Sozon and Agia Anastasia – and the fifth church, the church of the Virgin Mary, sits on top like a dome.

The church received its name Paraportiani, which means "standing next to the entrance / door", because it was located next to the entrance of the ancient castle, or kastro door. The neighbourhood of Kastro, where it is situated, used to be the site of a medieval castle – in those days a castle was a strong fortification surrounding a settlement – constructed in 1207 by the Gisi family, who controlled the island a the time. The castle was destroyed in the 16th century and its remnants covered up by new buildings when Chora began to expand in the 18th century.

It took around 200 years to build Panagia Paraportiani. Construction began in the 15th century and was not completed until the 17th century. The oldest of the five small churches is Agios Anargyros and the others gradually piled on top over the 16th and 17th centuries. There is a fascinating mixture of architectural styles: Byzantine, vernacular, traditional and western combine in a single monument.