The suggestion was approved of, and the Anglo-Benedictine authorities resolved to incorporate with the Scottish monastery Lamspringe Abbey, in Hanover, which was manned by English monks from 1645 to 1803.

Up to the year 1882 St Benedict's monastery remained under the jurisdiction of the Anglo-Benedictine Congregation, but in response to the wishes of the Scottish hierarchy, and of the leading Scottish nobility—notably Lords Lovat and Bute—Pope Leo XIII, by his Brief "Summâ cum animi lætitiâ", dated 12 December 1882, erected it into an independent abbey, immediately subject to the Holy See, thus separating it from English rule.

In 1888, Leo Linse of the Beuronese Benedictine Congregation, who had resided for more than ten years in England, part of that time as superior of Erdington Priory, near Birmingham, was nominated abbot by the Holy See and received the abbatial benediction at the hands of Ignatius Persico, Archbishop of Tamiathis, who had been sent to the abbey as Apostolic Visitor.

In 1993, owing to changing educational patterns in Scotland which caused a falling roll, Abbot Mark Dilworth decided to close the school.

It quickly became clear that a small business could never generate sufficient income to support the monks and the rambling Victorian buildings so a major project was begun.

The enterprises initially showed great promise, becoming a major tourism force in the Highlands, but it was discovered that the buildings required more costly repairs than had been envisaged.

[4] In 2013, The Observer newspaper reported that Scottish police were investigating allegations that pupils had been subject to physical and sexual abuse while at the abbey school.

[5] A BBC Scotland Investigates programme, entitled Sins of Our Fathers,[6] reported allegations that Fort Augustus Abbey was used as a "dumping ground" for clergy previously accused of abuse elsewhere.

In particular, five men were raped or sexually abused by Aidan Duggan, an Australian monk who taught at Carlekemp Priory School in North Berwick and Fort Augustus Abbey between 1953 and 1974.

The headmaster at the time refused to be interviewed for the BBC programme, but made a statement apologising to the victim and his family for Alexander's abuse.

[9] In 2017, Denis Alexander was arrested in Sydney, Australia, and faces an extradition for sexual and physical abuse he reportedly committed at Fort Augustus in the 1970s.

[13] Giving evidence to the Scottish Child Abuse Inquiry in July 2019, Seed was confronted about an admission he had made to Bishop Hugh Gilbert in 2013 about two indecent sexual relationships with minors at the school.

Both schools were havens for paedophiles where they had easy access to their chosen victims," concluding "there was a range of sexual abuse, including oral sex and sodomy.