Unfortunately, the unusual construction of the church caused problems with its roof. In 2022, mold was discovered in the carpet and HVAC system, necessitating the end of regular services. Repairs were found to cost as much as $1,000,000, and, with the Catholics of Hamden now being easily accommodated at three other churches, a closing Mass was held on October 15, 2023.
In addition to declining attendance, another factor for Catholic churches was a shortage of priests. The first Hamden churches affected were St. Ann and St. John the Baptist, which merged in 2004, sharing one pastor. (St. John, just over the city line in New Haven, was founded in Hamden in 1891.)
As part of a restructuring throughout the Archdiocese of Hartford in 2017, Blessed Sacrament, Ascension, St. Ann, and St. John merged into one parish, with the latter two churches closing; St. Rita and St. Stephen merged; and Our Lady of Mt. Carmel and St. Joan of Arc churches merged, the latter church closing. In 2020, the St. Rita – St. Stephen parish decided to close the latter church. The St. Stephen building was sold to Virgin Mary & Archangel Michael Coptic Orthodox Church, formerly on Benham Street.
A second round of restructuring throughout the Archdiocese began in 2022. All the churches within each municipality were to become one parish. The Hamden churches formed St. Paul VI Parish. Paul VI was pope when the St Rita, Ascension, and St. Joan of Arc churches were built.
Protestant churches too saw their share of consolidation. The oldest church building in Hamden, Grace Episcopal, was built on Dixwell Avenue in 1820. In 1966, the church building was moved directly across the avenue. In 1990, it merged with St. Peter's on the Hill to become Grace and St. Peter's. Another merger in 2022, with St. John the Evangelist in the Yalesville section of Wallingford, changed the name to Grace and St. John's.
The two Lutheran churches in Hamden, Christ Lutheran on Shepard Avenue and Lutheran Church of the Good Shepherd on Whitney Avenue, merged in 2021. The Shepard Avenue building became Christ the Good Shepherd Lutheran Church.
East Plains Congregational Church relocated from its 1795 meetinghouse on Dixwell Avenue to the corner of Whitney and Putnam avenues in 1834. Whitneyville Congregational Church was built there on land donated by the widow of Eli Whitney. The congregation remained viable for nearly two centuries, but by 2020 had dwindled so that it was unable to maintain the building. It was donated to a nonprofit organization, Whitneyville Cultural Commons, which raised funds for its restoration, completed in 2023. The organization is using the church and adjacent parish house for various events.