It is believed that in the early part of the 14th Century, Robert the Bruce, being out of favor with many of the Clan Chiefs and hunted by the English, was given refuge at Eilean Donan Castle. Later, in 1331, with his fortunes changed Robert the Bruce defeated his enemies and solidified his position as King of Scotland. The Clan MacRaes, who formed the bodyguard of the Chief of Kintail, first became Constables of the Castle in 1509. In 1539, Donald Gorm, a Lord of the Isles, led 400 warriors in an attack on the Castle. The acting Constable, Duncan MacRae, successfully defended the Castle and with his very last arrow, fatally wounded Donald Gorm.

In 1719, at the time of an unsuccessful Jacobite uprising in favor of the Old Pretender, a Spanish force was sent to Scotland and set up their headquarters at Eilean Donan. In May 1719, three English frigates sailed into Loch Alsh and attacked the Castle, which fell after a short bombardment of superior artillery fire. The stark ruins of the once proud Castle were to remain neglected for 200 years.