In the 1960s, decisions made during Vatican II changed the appearance of the interior of the chapel. The services within the Roman Catholic Church were transformed, so that the priests faced the congregation as they spoke, rather than turning to face the altar. This meant that some of the furniture at the front of the chapel was removed, or replaced to accommodate the new practices. The attitudes towards elaborate decoration within Catholic churches also changed at that time, with feelings that the decor should be simple.
The plans for the renovations were arranged at the Bishopís house and were executed by the maintenance men at the Academy. Much of the ornamental painting, including the gilded carvings, was painted over at St. Annís. The Stations of the Cross, the series of relief panels hanging on the side walls, were given a grey coat of paint to subdue their appearance. Many of the Sisters were torn by these changes. They wanted the new attitudes and thinking that went along with Vatican II, yet it hurt them to see their beloved chapel disturbed. A Sister spoke for many of the women at the convent at the time when she stated, "We thought this was a violation of history and archives." Yet, she also felt that the essential religious atmosphere had not changed because of those renovations of the 1960s.