The history of the Irish Church throughout the second millennium is in many respects rooted in the rise and decline of religious orders and of the survival of religious persecution. As a diocese Elphin proved fruitful soil for the religious life. By the late 15th / early 16th century it was home to at least eighteen religious houses, including the Canons Regular of St. Augustine, Benedictines, the Order of St. John of Jerusalem, Carmelites, Cistercians, Premonstratensians, Dominicans and Franciscans. However great changes were to follow, starting with the religious revolution of the 16th century and during related persecution the diocese lost many monasteries, convents and its Cathedral.
Following the Reformation, there were parallel dioceses. The Church of Ireland diocese continued from the 16th until the 19th century but since 1841 has been part of the united Diocese of Kilmore, Elphin and Ardagh. A new Church of Ireland bishop's palace (i.e. official residence) was built in the 1720s.
Elphin's mediaeval cathedral was also rebuilt in the eighteenth century. It was a modest building no bigger than a small parish church with a tall square clock tower at its west end. It was badly damaged in a storm in 1957 and was demolished a few years later, but its partially restored ruins can still be seen.