Following the outbreak of the Irish Rebellion of 1641, the Catholic Taaffe remained loyal to the authorities in Dublin.
After the Cromwellian conquest of Ireland, Taaffe accompanied Charles II in exile.
Theobald Taaffe was appointed to lead the Irish Munster army by Donagh MacCarthy, Viscount Muskerry in 1647.
He was not an impressive commander, failing to prevent the sack of Cashel and then leading the Munster army to defeat at the battle of Knocknanauss in 1647.
He had an antiquated sense of chivalry - before Knocknanuss he suggested to Baron Inchiquin, the enemy general, that the battle should be decided by 1000 hand-picked men from each side.