In 1878, Mary Andrew became headteacher, teaching French to the girls and insisting that they speak it at all meals and for certain hours in the evening; a fine was imposed on anyone who lapsed.
Pupils were expected to dress with 'a sense of propriety', and an early photograph shows the girls wearing ankle-length skirts and long-sleeved white blouses.
Following the sisters’ retirement, the newly formed Council appointed Mary C. Bell as the first headteacher of the new independent St Margaret's.
Electric lighting and a system of central heating were installed throughout, the big drawing-room was converted into a gymnasium and the assembly hall was turned into a library.
Miss Bell taught the girls of St Margaret's to think for themselves, to acquire a sense of responsibility and to have pride in their school.
Miss Bell's successor was Mabel E. Holland and, under her able direction, the school rode out the problems of disruption and evacuation caused by the Second World War.
On her arrival at school in August 1939, with the new session due to start, Miss Holland was greeted by the news that 17 Albyn Place had been requisitioned for the Food Office.
With the coming of war in 1939, the boarding houses were evacuated to the country, for the greater safety of the children and because the school’s buildings were requisitioned.
Here was remoteness indeed, especially for those in Glenbuchat Lodge, where the main road was seven miles away; a horse-drawn sledge was needed to deliver the groceries in the snowy winter of 1939.
In autumn 1947, (following the sale of the Queen's Gardens properties) the School Council purchased Culter House, which became home to many boarders for 41 years.
In 2015, the school completed its largest estate development in almost 20 years with the opening of its new state-of-the-art science block, which was officially opened by renowned British astrophysicist Dame Jocelyn Bell Burnell, who is credited with one of the most significant astronomical discoveries of the 20th century, that of radio pulsars.
This consists of a shield bearing the arms of St Margaret, Queen of Scotland, surmounted by the three triple-towered castles which symbolise the City of Aberdeen.
The motto below the shield is Tenez Ferme (hold fast), chosen at the suggestion of Dr Esslemont Adams, a member of the school's Council.