The original St Agatha church, similar to the Benedictine monastery, dates back to the early 15th century. It was built by the noble family Gatto Murina. The same family also built the church of St Paul in Rabat, the façade of which bears their name. The Gatto Murina family donated the St Agatha church in Mdina to the Diocese of Malta in the 17th century.
Malta was always closely connected to neighbouring Sicily and, with that, came the devotion to St Agatha. St Agatha, St Publius and St Paul are the three patron saints of Malta.