Long obliged to perform penance for his part in Dougall's assassination, John Moidartach made a vow to build a number of churches, including Kildonnan Chapel. By the time it was built, the Scottish reformation had occurred, and the Kildonnan Chapel is typical of the post-Reformation style. It was built directly on top of the site of one of the earlier monastic buildings. The fate of the original monastic chapel – which lay south of this – is unclear, but the reformation may have caused it to be abandoned and dismantled; indeed, the Kildonnan Chapel itself doesn't appear to have been finished. The statutes of Iona, in 1610, had introduced a programme of government oversight of the religious behaviour of highlands leaders; the Clan Ranald leader's consent to this had resulted in the king granting him a charter confirming his lairdship of Eigg (and his other possessions).
