Fitzmaurice launched his rebellion by attacking the English colony at Kerrycurihy south of Cork city in June 1569 before attacking Cork itself and those native lords who refused to join the rebellion. Fitzmaurice's force of up to 4,500 men went on to besiege Kilkenny, seat of the Earls of Ormonde in July. In response, Sidney mobilised 600 English troops, who marched south from Dublin and another 400 troops landed by sea in Cork. Thomas Butler, Earl of Ormonde returned from London, where he had been at court, brought the rebel Butlers out of the rebellion and mobilised Gaelic Irish clans antagonistic to the Geraldines. Together, Ormonde, Sidney and Humphrey Gilbert, appointed as governor of Munster, began devastating the lands of Fitzmaurice's allies. Fitzmaurice's forces broke up, as individual lords had to retire to defend their own territories. Gilbert in particular was notorious for the terror tactics he employed, killing civilians at random and setting up corridors of severed heads at the entrance to his camps.
Sidney forced Fitzmaurice into the mountains of Kerry, from where he launched hit and run attacks on the English and their allies. By 1570, most of Fitzmaurice's allies had submitted to Sidney. The most important, Donal MacCarthy Mor, surrendered in November 1569. Nevertheless, the guerrilla campaign dragged on for three more years. In February 1571, John Perrot was made Lord President of Munster, pursuing Fitzmaurice with 700 troops for over a year without success. Fitzmaurice had some victories, capturing an English ship near Kinsale and burning the town of Kilmallock in 1571, for example, but by early 1573, his force was reduced to less than 100 men. Fitzmaurice finally submitted on 23 February 1573, having negotiated a pardon for his life. However in 1574, he again became landless and in 1575 he sailed to France to seek help from the Catholic powers to start another rebellion.
Gerald FitzGerald, Earl of Desmond, and his brother John were released from prison to stabilise the situation and to reconstruct their shattered territory. Under a new settlement imposed after the rebellion, known as "composition", the Desmonds' military forces were limited by law to just 20 horsemen; their tenants were made to pay rent to them rather supply military service or to quarter their soldiers. Perhaps the biggest winner of the first Desmond Rebellion was the Earl of Ormonde, who established himself as loyal to the English Crown and as the most powerful lord in the south of Ireland.
Although all of the local chiefs had submitted by the end of the rebellion, the methods used to suppress it provoked lingering resentment, especially among the Irish mercenaries; gall oglaigh or "gallowglass" as the English termed them, who had rallied to Fitzmaurice. William Drury, the new Lord President of Munster from 1576, executed around 700 of them in the years after the rebellion. Furthermore, in the aftermath of the rebellion, Gaelic customs such as Brehon Laws, Irish dress, bardic poetry and the maintaining of private armies were again outlawed – things that were highly provocative to traditional Irish society. Fitzmaurice, by contrast, had deliberately emphasised the Gaelic character of the rebellion, wearing the Irish dress, speaking only Irish and referring to himself as the captain (taoiseach) of the Geraldines. Finally, Irish landowners continued to be threatened by the arrival of English colonists.[clarification needed] All of these factors meant that, when Fitzmaurice returned from continental Europe to start a new rebellion, there were plenty of discontented people in Munster waiting to join him.
In late 1569 a similar Catholic rebellion, the "Northern Rebellion," broke out in England, but was quickly crushed. This and the Desmond Rebellion caused Pope Pius V to issue Regnans in Excelsis, excommunicating Elizabeth and depriving her of the allegiance of her Catholic subjects, in early 1570. Elizabeth's regime had previously accepted discreet Roman Catholic worship in private; afterwards it suppressed organised Catholicism more severely.