Since the fifteenth century, it has been the site of many royal coronations and marriage ceremonies. It also suffered from a number of attacks. During "The Rough Wooing" by Henry VIII of England, Edward Seymour as Earl of Hertford plundered the abbey in 1544, then as Protector Somerset led a raid causing great damage to the buildings. King James VII established a College of Jesuits in Holyroodhouse and had the Abbey converted in May 1688 to become a Roman Catholic chapel for the Order of the Thistle, with the Protestant congregation being moved to the new Kirk of the Canongate, then in November of that year when the Glorious Revolution brought in William II, Prince of Orange the people of Edinburgh broke in to plunder the kirk and the royal burial vaults. In 1691 the Kirk of the Canongate replaced the Abbey as the local parish church. Restoration work included the roof of the abbey being rebuilt in 1758, but the roof collapsed in a hurricane in 1768, leaving it as it currently stands, a ruin.
Following the Disruption of 1843 in the Church of Scotland, part of the congregation of the Kirk of the Canongate left to form Holyrood Free Church. A new building was constructed in front of the Palace of Holyroodhouse. This congregation united with Abbeyhill United Free Church in 1915, henceforth using the Dalziel Place church buildings. The United Free Church of Scotland united with the Church of Scotland in 1929, the congregation henceforth being known as Holyrood Abbey Church. The building was extensively upgraded in 2006-2007.
Today, the Holyrood Abbey Church of Scotland congregation is well-known in Edinburgh for its Conservative Evangelical theology and tradition of expository preaching, developed by the Reverend James Philip MA (the congregation's former minister 1958-1997). Mr Philip was a friend of the Rev William Still, minister at Gilcomston South Church in Aberdeen from 1945 until 1997, the pioneer of expository preaching in the Church of Scotland. The current minister is the Rev Philip Hair BD.
The former Holyrood United Free Church building adjacent to the Palace was used for many years as a storeroom, but in 2003 was extensively renovated and reopened as "The Queen's Gallery" for art exhibitions from the Royal Collection.