Significant events in the history of the church are as follows: The First Easter Mass was held in 1521. A Mission was founded by the Jesuits in 1596. It was blessed as the First church built in Mindanao in 1597. St. Joseph was proclaimed as Titular Patron in 1622 and St. Francis de Sales as Second patron in 1792. The Blessing of the old parish church was done in 1883. The present church was consecrated in 1954 and was elevated as a cathedral by Pope Paul VI in 1967. It was appointed as the host church for the Great Jubilee in the year 2000 and was declared as a dedicated cathedral by Ricardo Cardinal Vidal in 2007.
On May 19, 2009, Rev. Father Siegfred Dosdos read the Decree of the Establishment of St. Joseph Cathedral as a Diocesan Shrine during the Pontifical Fiesta Mass that was approved by His Excellency Juan de Dios Mataflorida Pueblos, Catholic Bishop of Butuan and Parish Priest of the Cathedral.