What lies beneath or within those walls, however, is considerably older than the building suggests. This was once a corn mill, recorded on the first edition Ordnance Survey six-inch map of Ireland, and at some point between that mapping and the present day it was converted into a dwelling. Whether the current structure incorporates original medieval fabric or was simply built on the footprint of an earlier mill, possibly reusing some of its stonework, remains uncertain.

The mill's most legible survival is not the building itself but the mill race, the channel cut to divert water and drive the mill wheel, which extends into the surrounding fields in both directions. A mill race is essentially an artificial watercourse, engineered to deliver a controlled flow of water to a mill and carry it away again afterwards. At Clonmacnoise, this earthwork can be traced to the north-east of the Mill House for a distance of approximately 675 metres, and to the south-west for a further 380 metres, making it a substantial piece of medieval water management. It appears on the first edition OS map and remains clearly visible on aerial photographs, running through fields that have otherwise long since lost their industrial character. Clonmacnoise is best known as the site of one of Ireland's great early monastic settlements, and a working corn mill in its vicinity would have been entirely consistent with the self-sustaining economy such communities required and maintained over many centuries.