One of the expectations of the government was that the Plantation would serve to advance the Reformation in Ulster. While at an institutional level the beginnings of a Protestant infrastructure were emerging in the early seventeenth century, at grass-roots level the Reformation had made very little impact.

At an organisational level, nearly all of the escheated counties were divided between the five dioceses of Armagh, Clogher, Derry, Kilmore and Raphoe. That part of County Londonderry on the east side of the Bann was in Connor diocese, while a small portion of north-east County Armagh was in the diocese of Dromore.

The dioceses in turn were divided into parishes. For the most part, the medieval network of parishes continued in use after the Reformation. There had been a suggestion that a new network of parishes be created whereby each parish equated with a plantation proportion. However, this was never carried out.