The population of Llanllibio declined substantially during the Middle Ages as a result of the Black Death and changes in farming practice, amongst other factors, and the community that the church served effectively disappeared.

A survey of Anglesey conducted in 1352 records Llanllibio as a tir cyfrif township, a Welsh form of land tenure in which the inhabitants, who were generally few in number, were bondmen working for the lord in return for a small arable holding and some grazing rights.

Communities such as Llanllibio were affected by the Black Death, the destruction resulting from the revolt of Owen Glyndwr, by changes in land tenure, and by new farming practices that reduced the need for tied labour.

[1] According to Angharad Llwyd, a historian of Anglesey writing in 1833, the inhabitants of the area attended worship at St Edern's Church, Bodedern.

[5] A survey in 1937 by the Royal Commission on Ancient and Historical Monuments in Wales and Monmouthshire stated that "the church has entirely disappeared, but the foundations of the churchyard wall are still visible.