The Franciscan presence in Koper reaches as far back as the very beginnings of the Franciscan order since the first brothers came to Koper soon after the death of St. Francis of Assisi. In 1229 St. Anthony of Padua presumably visited the town. The hitherto known records mention the Order of the “Poverello of Assisi” in 1264 when the bishop of Koper allowed the Franciscans to build a new church because the old one was in a state of decay.
Also the renowned Franciscan lawyer and preacher Blessed Monaldus de Iustinopoli (da Capodistria) lived and worked in this friary (died around 1280).
The beginnings of the present church reach into the year 1492 when the Koper nobleman Antonio Almerigotto and his wife Chiara donated a plot of land to build a new church and monastery. They were completed and furnished by Christmas 1513. The church received its present look by the renovation finished in 1627. The friary was renovated in 1644.
From the very beginning the friary was intended as an education house and thus theology and philosophy studies were pursued there. In the 18th century it was declared a Studium generale and was entitled to grant the degree Lector theologiae that was acknowledged throughout the Order.
Until 1924, when in accordance with the Treaty of Rapallo it was taken over by Italian Franciscans, the monastery belonged to the Dalmatian Franciscan Province of St Jerome having its seat in Zadar. After the end of the Second World War, the Province of St. Jerome and the Slovenian Franciscan Province of the Holy Cross exchanged the monasteries of Pazin and Koper in 1953 and thus the Koper friary came into the possession of Slovenian Franciscans. A year thereafter the monastery was nationalized and turned into a prison. The Franciscans only kept the church and some outbuildings at the side of the church.
In 2004 the prison moved out of the monastery. The Franciscans immediately started to prepare renovation plans. A thorough renovation was started in 2006 and completed in 2008. The friary now hosts the Franciscan community, the students of the Student Residence Sidro and the Centre Rotunda – littoral social centre.