Over the centuries the Abbey buildings have been considerably altered. St Columba and his followers built a small monastery from wood, wattle and daub. Later, the timber was replaced with stone and in around 1200, the Columban Monastery was transformed into a Benedictine Abbey. Numerous additions were made to the building from then until the mid 16th Century. The architecture of the church was determined by the demands of its monastic community, local congregation and pilgrims, so its shape evolved to meet their needs.

It was here, at Iona Abbey, that the magnificent Book of Kells, undoubtedly one of the most beautiful artifacts of the Middle Ages, was made. And it was here that the Vikings launched their first raid in 795. They returned again and again through the course of the ninth century, and eventually the Book of Kells and other treasures were moved, although other relics of St. Columba were stolen or lost. The large Celtic crosses which had covered the landscape were eroded and toppled over. Once there had been nearly four hundred, in time only three remained.

Despite surviving many attacks from the Vikings, the Abbey was unable to escape the Reformation in 1560 and was left derelict. It remained so until, in 1899 when the Duke of Argyll transferred ownership of the buildings to the Iona Cathedral Trust (linked to the Church of Scotland). Unfortunately the gift of ownership to the public was not accompanied by any endowment and funds had to be raised by the Trust.

The Boer War had made such a heavy demand on the public purse that the first appeal for the restoration fund was not made until 1901. Work began the following year, re-roofing and re-glazing, for the sum of £2,750. Rebuilding continued as and when funds allowed, individual donors were often most generous and some have windows in the Abbey dedicated to them.

Restoration of the monastic buildings began in 1938 when Rev George F MacLeod established the Iona Community. The scheme was designed to unite craftsmen and trainee ministers in the task of renovating the monastery. Experiencing the physical renewal of the Abbey was intended to prepare the young ministers to achieve spiritual renewal when they returned to their inner city parishes. The monastery restoration was completed in 1965.

In recent years, the Iona Cathedral Trust found the financial burden of maintenance of the Abbey increasingly difficult. Historic Scotland have now taken on that burden and administer the Abbey structure and maintenance. As a result, there is an admission charge to help with the "up-keep". "Historic Scotland" also run the Abbey shop".