He died on 10 September 1547, aged 53, being slain at the Battle of Pinkie. His will included £50 owed to him by Mary of Guise, and in it he wished to be buried in his new church and his father's remains to be taken there from Boghall. Cumbernauld Castle went to his eldest son, James Fleming. His wife was to have Boghall excepting its artillery.