The Church of St Mary and St Peter is a church in Waddingham, Lincolnshire. It is a Grade II* listed building.
The church was built in the 13th-15th centuries and went under a renovation in 1858 by Revd Windsor Berry. There are currently three bells in the tower, made by George Heathcote, Humphrey Wilkinson and Daniel Heathcote.
The church went under a restoration in 1862, where a south porch had been built and roofs were added to the nave and aisles, and was reopened in 1864.