The oldest part of the present building is the south east corner, which dates back to the 12th century. The rest of the cathedral is a mixture of successive rebuilding and alterations dating from the 17th to late 19th centuries. A major restoration, virtually a re-building of the medieval cathedral was taken in hand by The Rt. Rev.Dr.George Montgomery around 1605. Montgomery had been chaplain to King James I, and was nominated not only Bishop of Raphoe, but of Clogher and Derry at the same time.
After centuries of modifications and restorations, much of the current building dates from the 1730s. The entrance is by the porch under the tower built in 1738 by Bishop Forster (1716-1744).
By the 1870s, the building had again become shabby and neglected. It attracted the unfavourable criticism of many church people and ecclesiologists. One high church architect, Sir Thomas Drew, described the cathedral as "the most neglected church in the diocese though situated in the richest part of Donegal."
In 1892 Drew was commissioned to begin a plan of restoration which uncovered much of the medieval fabric while "medievalizing" the greater part of the rest of the building. The cathedral retains the characteristic of many such medieval buildings where larger bodies of clergy offered more elaborate liturgies in that the quire or chancel is longer than the nave.