In 1644, during the Civil War, Prince Rupert left a garrison at the castle on his way to relieve the parliamentarian siege of York. They repaired the main gateway and stocked the castle with provisions, only to abandon it following the royalist loss at the Battle of Marston Moor. When the Lancashire militia was ordered to disband in 1649, they refused, occupying the castle for a brief period in a dispute over unpaid wages. The same year Clitheroe was among a number of castles that parliament decided should be 'slighted' to prevent further use, although it is uncertain what demolition work actually resulted.