During the closing stages of the war between England and the Ulster lords, the castle suffered much damage, sometimes by English attackers and sometimes by the Irish, including the Maguires themselves, to prevent it from being used by the English.
In 1602, Hugh’s successor as chieftain, Cuchonnacht Maguire, destroyed the castle, again to prevent the English army from setting up a base there.
With the peace settlement which followed the defeat of the Ulster rebels, Cuchonnacht Maguire was pardoned and an arrangement was made for him to receive half of county Fermanagh, including Enniskillen Castle, with the other half going to Conor Roe, head of the Lisnaskea branch of the Maguires.
However, in 1607, when Cuchonnact Maguire organised the so-called Flight of the Earls and left Ireland with the other Gaelic leaders, he was deemed a traitor and his lands were confiscated. With the castle now in English hands, Captain (later Sir) William Cole was put in charge and tasked with using the remnants of the Maguire tower-house to make the site a workable garrison fort.