In a room sequestered to the right of the main body of the church are some of the sacred remains of St. Margaret, Queen of Scotland. An arduous and lengthy campaign began in the middle of the 19th-century to retrieve what was left of her scattered remains. During the Scottish Protestant Reformation in 1560, Dunfermline Abbey was ransacked. Many Scottish nobles were interred here, including St. Margaret and Robert the Bruce.

To preserve the remains, individual skeletal parts were scattered throughout mainland Europe. A piece of her shoulder bone was traced to Madrid, under the protection of King Phillip II of Spain. It would take until 1862 when Pope Pius IX, with the permission of Queen Isabella II, allowed Scottish bishop James Gillis to return to Scotland with her remains. They were kept under the care of the Ursuline Sisters at St. Margaret's Convent in Edinburgh until 2008 when they were moved to their current location.

St. Margaret, known as 'The Pearl of Scotland," was originally from Hungary and married King Malcolm III of Scotland in 1070. They had eight children, all six of the boys became Kings of Scotland and one of her two daughters, Edith, was crowned Queen Matilda of England. Margaret was canonized in 1250 by Pope Innocent IV. She is Scotland's only female saint.

Besides looking after those less fortunate than herself, Margaret was known for her charity toward orphans. She was responsible for the preservation and upkeep of monasteries and other houses of worship throughout Scotland. Her largest contribution was providing a safe ferry service to the thousands of devotees, who made pilgrimages across the Firth of Forth, in order to pay homage to another holy person's reliquary, that of St. Andrew. This is where the ports of North and South Queensferry derive their name.