The territories of the MacCarthy dynasty in north west Cork, together with the kingdoms of Fermoy and Imokilly, came to make up the new diocese of Cloyne.

Robbery of church property by nobles impoverished the Sees of Cloyne and Cork, which were united in 1429, by papal authority, under Bishop Purcell.

The bishops of penal times were ruthlessly persecuted, and some suffered cruel imprisonment or died in exile.

[5] John O'Brien author of an Irish dictionary, poems, and tracts, was Bishop of Cloyne and Ross from 1748 to 1769.

[6] Since 1769 the Bishops of Cloyne, with the exception of Dr. Timothy Murphy, resided at Cobh (formerly Queenstown) on the north side of Cork Harbour.

Following the relaxation of the worst elements of the Penal laws, "...the diocese, despoiled of all its ancient churches, schools, and religious houses, had to be fully equipped anew.

"[5] Following the separation of Ross, Bishop William Keane planned a cathedral for Cobh to replace the inadequate parish Church of the time.

Archbishop Daniel Mannix of Melbourne was born in Charleville in 1864 and ordained for the diocese of Cloyne in 1890.

Nominated Bishop of Cloyne in 1894, his principal task was to complete the building of Cobh Cathedral which he consecrated in 1919.

Bartholomew MacCarthy, Celtic scholar and editor of the Stowe Missal, was born at Conna, Ballynoe, County Cork in 1843.

According to a Health Service Executive (HSE) audit, the then Vicar General Denis O'Callaghan as the person responsible and the Diocese had put children at risk of harm through an "inability" to respond appropriately to abuse allegations and "had taken a fairly minimalistic role in terms of sharing information with the Board".

[13] On 4 February 2010, Bishop John Magee requested Pope Benedict to relieve him of his duties, saying that he would use the time to "devote the necessary time and energy to cooperating fully with the government Commission of Inquiry into child protection practices and procedures in the diocese of Cloyne" which up to this point had been handled by Denis O'Callaghan.

Bishop Magee now resides in a North Cork town and is frequently invited to presided at various religious and Eucharistic celebrations overseas, particularly in Italy.