Partney must have been one of the earliest centres of Christianity in Lindsey. There was a monastery here at the time of Bede, the historian of Anglo-Saxon England c. 700A.D. There is no reference to the Church in the Domesday book but that there was a church in Partney at that time cannot well be disputed, since Gilbert de Gaunt, who died about 1090, granted it to the Abbey of Bardney. This grant was confirmed by Gilbert's successors and in 1292 we find a definite reference to "the church of Saint Nicholas at Partney".
The oldest parts of the present building date from the first half of the 14th century. Its finest features are the capitals of the pillars on the south side of the nave. These are richly carved and former a contrast with the much plainer capitals on the north side.
The church was evidently rebuilt in part during the 15th century. To this period belong the tower with its tall and graceful arch, the west window, the chancel window and the font. The clerestory also was added at this time, the nave roof having previously been much lower.
The church was thoroughly restored about 1860. The nave and aisles were completely rebuilt, though much of the existing stonework was used again, and a new porch was added. The church is dedicated to the glory of God and in honour of St Nicholas, Bishop of Myra in Asia Minor during the 4th century. St Nicholas is the patron saint of fishermen and children. The churchyard contains a stone commemorating the marriage of Matthew Flinders, the first circumnavigator of Australia, and Ann Chappelle on 17th April 1801.