The original building was the Free Church Manse constructed in 1846-47 and occupied by the Rev. Donald McVean and his family. The architect was Rowan Anderson who supervised the first restoration of the Abbey in 1874. The Duke of Argyll did not renew the lease and on the 9th May 1868 the following advertisement appeared in the Oban Times: "Island of Iona. Notice of house to let". Two public and six bedrooms. Well adapted for the accommodation of travellers. Well worthy the attention of persons accustomed to the management of inns or lodging houses. There is a walled garden well stocked with fruit trees, and some parks with grazing, if required, can be added."
The earliest known picture of the building was depicted in The Antiquities of Iona, a book by Mr. H.D. Graham, published in 1850. Mr. Graham stayed in the house as a guest of the McVean family between 1847 and 1852.
On the 25th May 1868 the lease was signed over to Captain and Mrs. George Ritchie. Captain Ritchie had previously been operating coastal smacks from Tobermory, where he ran the Mishnish Hotel. The Ritchie family ran the Manse as a hotel until 1902 when it was taken over by Mrs. MacKenzie and her son, who came from Skye.</p>
The MacKenzies were the first people to make an addition to the hotel and the photograph shows the buildings as they were in 1926, with a new dining room annex to the south, and a separate northern annex (just showing) of four bedrooms in the north wing.</p>
In 1942 the hotel was taken over by Mr. and Mrs. MacDougal, and then passed into the hands of Mr. and Mrs. Walter Tindal in 1946. Mr. Tindal extended the main building to the north in 1957, creating the north wing, which incorporated the old separate annex.
The Columba Farm used to be linked to the hotel, but was separated from it when the hotel was bought by John and Dorothy Walters in 1965 although Mr. and Mrs. Tindal continued to have the tenancy of the farm. We do not know at what point the hotel ownership passed to the proprietors, rather than just being leased from the Duke of Argyll; but it was about this time that the Duke and Duchess of Argyll had exercised their right of pre-emption, but relinquished it, after they failed to get a drinks licence. In 1967 the old dining room was demolished and the present timber structure was erected.
Angus and Alison Johnston bought the hotel and ran it for 25 years, 17 of them in partnership with Teal Picton Phillipps.
The hotel was bought by SCH Iona Ltd. SCH was a consortium of individuals who had previously visited the hotel for conferences.
Hotel bought by St. Columba Hotel Ltd., an island based partnership of ten individuals nine of whom live and work on Iona.