He subsequently served the royalist cause of the House of Stuart as an army officer in the Cromwellian conquest of Ireland.
As Colonel Moore, he was among the royalist commanders in Connacht who surrendered to parliamentary authority in July 1652.
Alongside Carlingford, he was accused of involvement in the Popish Plot in 1681, but does not appear to have suffered any consequences.
Moore is recorded as having written to James II to warn him of the extremism of Richard Talbot, 1st Earl of Tyrconnell.
He served in the Irish Jacobite army during the Williamite War in Ireland as the colonel of a free company.