In 1584, he accompanied the lord deputy, Sir John Perrot, on the government's campaign in Ulster against Sorley Boy MacDonnell, and was commended for his valour after receiving a wound.
In April 1587, after Perrot's departure for England, Fitzgibbon was arrested by the government; the advice of Sir Anthony St Leger, to make him, "shorter by the length of his head" was not taken, and in 1589 he was released on heavy recognizances.
There were suspicions of his complicity with the rebel Hugh O'Neill, during the Nine Years war (1595-1603: see Essex in Ireland), but he submitted unconditionally to Sir George Thornton in May 1600 and blamed his folly on his son John, who had joined the crown's enemies.
Doubts about his loyalty were raised at the highest point of the war, when he failed to capture the Súgan Earl of Desmond, James FitzThomas FitzGerald, as the rebel nobleman passed through Fitzgibbon's territory in May 1601, but Carew was happy enough with his conduct after that.
He did at last manage to capture the Súgan Earl of Desmond in caves near Mitchelstown, and in reward Elizabeth I carried out the full restoration, by an act of parliament, of his lands and lineage.