Flora was born in Milton, South Uist, one of the Outer Hebridean Islands to the west of Skye. After the death of her father Ranald MacDonald, her mother married Hugh MacDonald, a member of the house of Sleat. She was brought up on Skye and attended school in Sleat and then Edinburgh.

Flora was visiting Milton when she became involved in the plan to help Bonnie Prince Charlie escape his pursuers.

After Charles's escape, Flora was taken to London and held in protective custody until July 1747. She was widely admired for her courage and money was quickly raised which enabled her to return to Edinburgh and then Skye.

She married Allan MacDonald of Kingsburgh. They lived at Flodigarry and raised a family. In 1774 they emigrated to North Carolina.

Flora returned to Skye in 1779 whilst her husband and two sons fought in the American War of Independence. After her husbands return they lived at Kingsburgh.

She died at Peinduin and it is said that over 3000 mourners attended her funeral at which 300 gallons of whisky were drunk. She was buried in the graveyard at Kilmuir.