Cefnllys was not directly attacked in the ensuing conflict but formed part of a chain of garrisoned castles encircling Llywelyn's territories, which contributed to the rebellion's suppression. Roger died in 1282 and his heir, Edmund Mortimer, 2nd Baron Mortimer, paid for a garrison of 8 horsemen and 20 footmen throughout the second phase of fighting (1282–3). In October 1294, Cefnllys was listed as one of the castles captured by "Rees ap Morgan" during the revolt of Madog ap Llywelyn, although the archaeologists David Browne &amp; Alastair Pearson have expressed uncertainty over this account. In 1306, the castle passed into the hands of Roger Mortimer, 1st Earl of March, who led an unsuccessful rebellion against Edward II which resulted in the confiscation of his holdings, including Cefnllys, in 1322. Roger returned from exile in 1326 and successfully overthrew Edward, briefly becoming "de facto" ruler of England alongside Queen Isabella, until he was executed in 1330 by Edward III. Cefnllys was forfeited by the Mortimers as punishment but returned to the family the following year. Repairs of the castle and its hall were carried out from 1356 to 1357, and at the outbreak of the Welsh uprising led by Owain Glyndŵr in 1400, Cefnllys was in temporary royal custody. Records show that it was defended by a well-provisioned force of 12 spearmen and 30 archersa detailed register of supplies sent to the castle in 1403 survives. This may have been insufficient, as a 1405 grant to Richard Grey described the lordship as "burned and wasted by the Welsh rebels", though it is unclear whether the castle itself was sacked or if the destruction was limited to its hinterland.