The commander of the local militia was her stepfather, Hugh MacDonald. The commander gave her a pass to the mainland for herself, a manservant, an Irish spinning maid, Betty Burke, and a boat's crew of six men. The prince was disguised as Betty Burke. He had left Benbecula on 27 June. After a first repulse at Waternish, Skye, the party landed at Kilbride, Skye, within easy access of Monkstadt, the seat of Sir Alexander MacDonald. The prince was hidden in rocks while Flora MacDonald found help for him in the neighbourhood. It was arranged that he be taken to Portree, Skye and from there taken to Glam on the island of Raasay. The talk of the boatmen brought suspicion on Flora MacDonald, and she was arrested and brought to London, England, for aiding the prince's escape. After a short imprisonment in the Tower of London, she was allowed to live outside of it, under the guard of a jailer. When the Act of Indemnity was passed in 1747 she was released.
On 6 November 1750, at the age of 28, she married Allan MacDonald of Kingsburgh, a captain in the army and the eldest son of Alexander MacDonald VI. The couple lived at Flodigarry on the Isle of Skye where they subsequently were parents to five sons and two daughters. Upon the death of Allan MacDonald's father in 1772, the family moved into the MacDonald family estate at Kingsburgh.
In 1774, she and her husband emigrated to North Carolina. During the American War of Independence Captain MacDonald served the British government in the 84th Regiment of Foot Royal Highland Emigrants. Legend has it that she exhorted the Loyalist force at Cross Creek, North Carolina, present-day Fayetteville, that included her husband, Allan, as it headed off to its eventual defeat at the Battle of Moore's Creek Bridge in February, 1776.
He was captured after the battle and was held prisoner for two years until a prisoner exchange occurred in 1777. He was then sent to Fort Edward in Windsor, Nova Scotia where he took command of the 84th Regiment of Foot (Royal Highland Emigrants), Second Battalion. After her husband was taken prisoner, Flora remained in hiding while the American Patriots ravaged her family plantation and took all her possessions. When her husband was released from prison during the fall of 1778, she reunited with him at Fort Edward.
In 1779 Flora returned home to Scotland in a merchant ship. During the passage, the ship was attacked by a privateer. She refused to leave the deck during the attack and was wounded in the arm. Flora resided at the homes of various family members, including Dunvegan, her daughter Anne having married Major General Alexander Macleod. After the war, in 1784, Allan also returned and the family regained possession of the estate in Kingsburgh. Flora MacDonald had a large family of sons, who mostly entered the army or navy, and two daughters. She died at Kingsburgh on the Isle of Skye, Inner Hebrides, in 1790, at the age of 68. She is buried in the Kilmuir Cemetery.
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