One is a sacristy, fitted with three aumbrys, shallow recesses cut into the wall to hold liturgical vessels. The other is stranger: a stone-roofed room accessible only through a low rectangular opening set more than a metre above the floor, its interior revealing a pointed arched vault and traces of mortar still bearing the impressions of the wicker framework used in its construction. It may have been a tomb, or it may have been a reliquary shrine where pilgrims could peer in at sacred objects. Nobody is entirely certain.

The site's importance stretches back, by tradition at least, to the 5th century, when the 7th-century biographer Tírechán credited St Patrick with founding the first church here and appointing St Senach as its bishop. What made Aghagower significant across the medieval period, though, was geography. It sat midway along an ancient routeway that became, in time, the Togher Patrick, a well-travelled pilgrimage road linking Ballintober Abbey to Croagh Patrick. As a principal stopping point on that route, the monastery grew in influence until it was counted among the foremost ecclesiastical centres in Mayo. By the late 11th or 12th century it had the resources to raise a round tower, still standing just three metres to the southwest of the church. The Annals of the Four Masters record the killing of the airchinneach, meaning the church official or erenagh, of Aghagower in 1094 by the men of Ceara. The Annals of Connacht eulogise his counterpart Donn Cathaig, who died on 15th December 1233, in terms that speak to real local authority: 'the reconciler of all disputes between his own household and the public in general.' A few years later, in 1247, another erenagh was treacherously killed at the festival of the Cross, and in 1248 John d'Exeter passed through with an army suppressing a Gaelic revolt in south-west Mayo. By the early 13th century the site had become one of the episcopal manors of the Archbishop of Tuam, and in the Taxation of 1306 it was assessed at the notably high value of £4.

The fabric of the surviving church is itself a layered document. The south wall carries a Romanesque-style doorway with a round-headed sandstone arch, suggesting a late 12th or early 13th-century date, while the tall east window, with its trio of round-headed lancets and switch-line tracery, belongs to the 15th century. Small carved human heads appear twice: once tucked into the hood moulding of a south wall window, wearing what may be a form of headgear indicated by a raised horizontal band across the forehead, and once on the northernmost mullion of the great east window. The collapsed west gable, now buried under centuries of accumulated graveyard soil, preserves traces of an earlier doorway that may predate the entire standing structure. Thirty metres to the south, within the same graveyard, lies a penitential station known as Labba Patrick, and two holy wells sit just outside the graveyard wall to the northwest.