The cathedral was extensively renovated beginning in 1980 under the direction of Frank Kacmarcik. The pipe organ was installed in the apse and dedicated in 1984. The Mother of Perpetual Help Shrine in the lower church was destroyed in a fire that did extensive damage to the lower church and smoke damage to the upper church. The lower church was renovated to create a chapel for Mass during the week, as well as a Eucharistic chapel and a gathering space. Five terra cotta disks that portrayed the "crux gammata" or swastika, an ancient stylized cross, were removed from the exterior of the cathedral in 2006. Because of its association with the Nazi Party in Germany, the parish determined the "crux gammata" could never recover its association with the Cross of Christ. They were replaced by five new limestone disks that depict the Luminous Mysteries that were composed by Pope John Paul II. The cathedral was refurbished in 2013 with a new floor, interior paint, and refurbishing the pews and kneelers.