Cloyne sat on a coast that was open to Norse raiders, and it paid the price seven times over. Between 822 and 1137 there are seven recorded devastations of the monastic settlement. The worst happened in 888, when Fergal, the Abbot-Bishop of Cloyne, was massacred by Danes. Each time the buildings were rebuilt and the community reformed, and each time the same coastline drew the same longships. The 12th-century Synod of Kells in 1152 finally regularised the Irish church under twelve suffragan sees subordinate to the metropolitan archdiocese of Cashel. Cloyne was confirmed as one of those twelve. Its territory came to include the MacCarthy dynasty lands in north-west Cork along with the petty kingdoms of Fermoy and Imokilly. Lismore diocese, on the other side of the Blackwater, was pruned back severely at Kells; it lost virtually all its County Cork jurisdiction except for Kilworth parish.

From 1429 until 1747 Cloyne was united with the Diocese of Cork by papal authority, after church robbery by local nobles had impoverished both sees. Bishop Purcell took on the combined dioceses. The Blessed Thaddeus MacCarthy held the position from 1490 to 1492. The Reformation brought disaster. The Penal Laws of the 17th and 18th centuries persecuted Catholic bishops directly - some were imprisoned, others fled into exile and died abroad. John O'Brien, the celebrated Irish lexicographer and Bishop of Cloyne and Ross from 1748 to 1769, finished his life in Lyons. After 1769 the bishops moved their residence to Cobh (then called Queenstown) on the north shore of Cork Harbour - a strategic relocation closer to the main population centre and the new cathedral that would eventually rise above it. Cloyne and Ross were separated in 1850, leaving the modern boundaries of the diocese roughly as they stand today.

With the gradual relaxation of the worst Penal Laws in the late 18th and early 19th centuries, the Catholic Church could legally rebuild. A diocesan history captures the scale of the work: 'the diocese, despoiled of all its ancient churches, schools, and religious houses, had to be fully equipped anew. About 100 plain churches were erected between 1800 and 1850.' These are the small, severe, slate-roofed chapels you still find in every village of east Cork - built before the great Gothic Revival of the late Victorian decades, before money or confidence permitted elaborate architecture. The grandest expression came later. Bishop Robert Browne, who took the see in 1894, devoted his career to completing the soaring spire of Cobh Cathedral - St Colman's - which he finally consecrated in 1919, fifty-one years after the foundation stone was laid.

The diocese sent priests out into the wider Catholic world. Three names recur in any history. Archbishop Daniel Mannix - born in Charleville in 1864, ordained for Cloyne in 1890 - went on to become Archbishop of Melbourne for forty-six years, from 1917 to 1963. His outspoken opposition to British policy in Ireland and his role in Australian politics made him one of the most contentious religious figures of the early twentieth century. Archbishop Thomas Croke - born at Castlecor in 1824, ordained at Paris in 1847, made first Bishop of Auckland in 1870 and then Archbishop of Cashel from 1875 until his death in 1902 - gave his name to the headquarters of Gaelic football and hurling: Croke Park in Dublin. Bishop Robert Browne, born in Charleville in 1844 and consecrated bishop of his home diocese in 1894, presided over the completion of Cobh Cathedral and died in 1935 having spent forty-one years rebuilding what the Penal Laws had taken away. Canon Patrick Augustine Sheehan of Doneraile, an enormously popular novelist between 1881 and 1913, wrote essays, short stories, poems and novels that were read across the English-speaking Catholic world.

In 2009 the Health Service Executive completed an audit of how the diocese had handled allegations of child sexual abuse by priests. The findings were grim. The HSE concluded that the then Vicar General, Denis O'Callaghan - the senior cleric who had been delegated responsibility for child protection - and the diocese as a whole had put children at risk through an 'inability' to respond appropriately to abuse allegations, and had taken 'a fairly minimalistic role in terms of sharing information with the Board.' The diocese accepted the findings. A government Commission of Inquiry produced the Cloyne Report in 2010, examining child protection practices and procedures in detail. Bishop John Magee, the long-time bishop and former private secretary to three popes, initially stepped back from his duties in February 2010 and resigned on 24 March 2010 upon learning the full gravity of the report's findings. He continues to reside in north Cork. The Cloyne case became a focal point of a national reckoning with how the Irish Catholic Church had failed children entrusted to its care. Bishop William Crean was appointed by Pope Benedict XVI on 24 November 2012 - Colman's feast day - and installed on 27 January 2013. The diocese continues its parish life, pilgrimages to Lourdes, Fatima and Knock, scripture programmes, catechist training. The work goes on around a wound the institution itself cannot heal.