Charlemont Fort retained its military significance after Tyrone's Rebellion came to an end. Caulfeild rebuilt the defences in 1622, adding a three-storied governor's house. At the outbreak of the 1641 Rebellion, the fort was taken by Sir Phelim O'Neill in a surprise attack. A number of attempts were made to recapture it, but despite the efforts of both Royalists and Covenanters it remained in O'Neill's hands until 1650, when a Cromwellian force ousted him after a bloody siege.