The Byzantine Museum is housed in the complex of buildings of Ekatontapyliani and contains numerous relics, coming from the church itself and from other churches of Paros. The collection started to build up in early 20th century when the archimandrite Georgios Skaramangas (1867-1944) was the parish priest of the church. There had been collected icons, sacred and precious objects from other churches of Paroikia. Later on and up to now, the collection is being enriched through donations of religious people and purchase of sacred relics. Initially, the collection was housed in the cells of the ground floor of the northern wing and was called Byzantine Museum of Paros.

The Museum was arranged and organized by the archaeologist Varoucha Christodoulopoulou, who was from Paros. After the death of the archimandrite in 1944 the museum closed. The collection was temporarily moved in three cells of the first floor and remained for a short time. After the death of bishop Epiphanios the museum closed again. The exhibits were gathered in a storehouse and during the years 1967 and 1981 several icons were restored, a work that continued after 1993 when the rest of the icons were also restored and the collection was partly displayed to the public.

On the 21st of May 1996, on the anniversary of the 1700 years of the church, the collection was exhibited almost in total, in three rooms of the ground floor. The exhibits are mainly woodcarved work, icons and a few samples of religious silver work. The rest of the relics are safely kept in a cell, they are being restored and it has been planned to display them as well.