He was appointed Deputy Governor of Beaumaris Castle on 30 August 1650 and received a commission to be "captain of a troop of horse of the Militia Forces to be raised in cos. Carnarvon and Anglesea" on 9 November 1650.
The Whitehall Committee was ordered on 8 July 1653 to put him and others into possession of the house late Dennis Bond.
There were further orders on 14 October 1656 for "Hugh Courtney, prisoner in the Isle of Wight, to be discharged",[3] and on 27 September 1658 for his release.
[3] On 13 April 1660 the Council of State issued a warrant to Serjeant James Norfolk to apprehend Courtenay and bring him in custody before the Council, and the next day ordered the Serjeant by another warrant to receive into custody in Lambeth House, Adjutant General William Allen and Hugh Courtenay "for endeavouring to debauch some of the soldiers from their obedience, and otherwise suspected of being dangerous to the State".
On 19 June 1661 Secretary Nicholas ordered their release from the Gatehouse, on security of £1,000 to leave the kingdom within 15 days.