The Domesday book records two churches in Threekingham; St. Peter and St. Mary. The church of St. Mary was at Stow Green, about half a mile away to the south east. The church has long gone but the site remains.

The remaining church of St. Peter has late Norman work in it, but no Saxon or early Norman work survives. It was clearly a very large and important church which has been altered so many times over the centuries that its origins and history are difficult to unravel.

The best evidence for the Norman work is the group of fine tall east windows in the chancel, with round heads and beautiful mouldings inside. The openings continued on the north side into a chapel that has been since demolished. The blocked arches to this chapel can best be seen outside. The rubble stonework at the base of the tower is also Norman, as are the large circular bases to some of the pillars of the nave arcades. The piers that stand on these bases are off-centre and do not line up with each other - clear signs of later building work being fitted into an existing structure.

The upper parts of the tower and its wonderful broach spire are 13th-century. The spire reaches a height of 145 feet. If you look at the east wall of the tower, you can see the line of the earliest nave roof which was more steeply pitched than the present low pitched lead roof.

Externally the aisle roofs are hidden behind parapets. The walls have large windows with flowing tracery, characteristic of the 14th-century style. Within the church the nave arcades have round or quatrefoil piers and simple pointed arches. The nave roof is a good example of a plain Lincolnshire oak roof dating from the late 15th-century. The principal members over the chancel are slightly moulded, and you can see that the roof timbers have been carefully repaired over the years.

The south porch is 14th-century and has a pair of feet inscribed in the stonework beside the door - one with a pointed shoe of medieval form. The door is covered with decorative ironwork dating from the 14th-century, taken off the original door when it was replaced in Victorian times.

The chancel has been well fitted internally in the 1920s. In the side walls are cupboards with stylish round arched openings and leaf shaped hinges of 'Art Deco' appearance. The panelling and reredos behind the altar are part of the same scheme of fittings. The nave pews look Victorian but their ends, set in later frames, are lovely examples of medieval carvings with vigourous traceried and foliage patterns of high quality.

The church has some good early monuments. The most notable is the huge knight and his lady at the west end. Larger than life these stone effigies depict Lambert de Trikingham and his wife who died about 1310. The details of their clothing repay close examination, not also the pair of lions at his feet and the puppies at hers. His wife is thought to have been one of the De Spayne family from the nearby hamlet of Spanby. Nearby are three large 14th-century slabs, also to the Trikingham family.

Near the organ is a handsome marble wall monument to William Fisher, complete with flutings, scrolls and urns and in the south aisle is a distinguished slate memorial to Edward Dawson, d.1787 with well cut lettering.

The simple tub font with trefoil headed decoration of about 1200 is inscribed at its foot with 'Ave Maria P.D.T.' meaning 'Hail Mary, full of grace, the Lord is with thee'.