In 1750, at the age of 28, Flora married Captain Allan Macdonald of Kingsburgh, and in 1773 together they emigrated to Montgomery County (formerly Anson), North Carolina. Flora actively participated in recruiting men for the 84th Highland Regiment, displaying once more her resolution. She exhorted the 84th Regiment at Cross Creek, North Carolina (present-day Fayetteville) before they went off to fight in the Battle of Moore's Creek Bridge. After Flora's husband was taken prisoner, Flora remained in hiding while the American Patriots ravaged her family plantation and she lost all her possessions. When her husband was released from prison, she travelled with him out of North Carolina to New York and then to Fort Edward in Windsor, Nova Scotia, in the fall of 1778. Flora only stayed in Nova Scotia for one year at Fort Edward, Windsor. In 1779 Flora returned home to Dunvegan Castle in Isle of Skye, Scotland. After the war, in 1784, Allan followed her.