Carbery's moment of victory was short-lived. The Parliamentarian forces in Pembroke rose up under John Poyer, and Carbery was forced to formulate a military response. Lacking any experience or natural aptitude as a soldier, he was limited to calling out his militia and laying siege to Pembroke, hoping to blockade the town into surrender. The Parliamentarian force resisted, at first being relieved by sea, and then launching attacks on the encircling Royalist strongholds, their forces led by Rowland Laugharne. Lacking a mobile reserve force, Carbery could do little to stop them, and soon had lost Tenby, followed by the entirety of Pembrokeshire by March 1644. Carbery was recalled to answer for the disaster, which worsened after his departure as Parliamentarian forces secured Carmarthenshire and Cardiganshire. Although he was exonerated from blame he was required to resign his commission, which was passed to Sir Charles Gerard. Carbery was assigned as Gerard's adviser, and returned to Wales in May 1644, but seems to have retired from any active role in military operations for the rest of the war.