Like most of the religious orders, the Franciscans were suppressed between 1539/48 and most of the buildings were knocked. Edmund Sexton got the land when it was confiscated. Some of the Franciscans stayed around the city after the suppression. The Franciscans took possession of their house in 1642 during the Confederate war. There was also an oratory to St Anthony on the island in what is now called St Mary's parish.
Over the years three chalices were given to the order - the Farrell Chalice (1619), the Creagh Chalice (1627) and the Rice Chalice (1626). The Creagh Chalice is now in the possession of the Bishop of Killaloe while the other chalices are still in use in the Friary.
On July 17th 1651, the Blessed Virgin Mary reputedly appeared over St Mary's Cathedral with St Francis and St Dominic as well as other friars from the two orders. The vision in the sky then moved onto the Dominican Priory and finally to the Franciscan church.
In 1687 the Franciscans rented the site of their old abbey from a descendant of Sexton, a man called Pery. It is believed that they remained at this site until 1691. By 1698 all religious orders had been expelled from Limerick city. By 1732 the Franciscans had moved to Burke's House in Athlunkard St. In 1745 Fr James White erected a small chapel at this location.
On Christmas Day, 1782 the Franciscans opened a small chapel in Newgate Lane, behind St Mary's Cathedral. A window from this chapel is now in Kilrush church ruin on the North Circular Road. This chapel remained in use until 1822 when the lease expired and the landlord, Major George P. Drew told the Franciscans that he would not renew the lease. The Franciscans took the church fittings with them and the building was then destroyed.
The Franciscans had a temporary house and chapel in Bank Place in 1825. They acquired ground in Henry St at a cost of £53 and began to build a church in 1824/25. The architect for the building was Mr O'Brien and the builders were Raleigh and Slattery. However they ran into trouble with the financing of the building. Many individuals gave money for the completion of the church and Dr. Laffan, the Archbishop of Cashel, blessed it on March 18th 1826. The church was opened to the public in May 1827. Over the next few years, a sanctuary was built and a belfry was added in 1837.