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Grade II* listed.

The church dates back to the 13th C. It has a western tower, nave with north and south aisles, the arcades of 3 bays are 13th Century, and chancel, vestry and porch. The tower was built in 1768.
St Mary's was burnt down in 1442; the tower was rebuilt in 1768 and the body of the church in 1823 and it has not changed much since then. The east end is shaped like five sides of an octagon and is very unusual. A choir vestry was added in 1921 and was later extended to include kitchen and toilet facilities. During the building of the vestry it was discovered that the original body of the church went six feet further north.
The church contains a hatchment dated 1838. At one time there was a gallery up against the west wall but it was removed in 1876 and at the same time the old box-pews were replaced with the present pine benches. The gallery would have been used for an orchestra up until 1851.

In the north aisle there is a stained glass window by Burlison & Grylls commemorating Royal Air Force personnel who served in the First World War and another depicting Dr Richard Smith, founder of Christ Hospital school in Lincoln.

The chancel screen was erected in 1907 and the furnishings of the chancel and sanctuary are mainly as they were arranged in 1860. In the chancel are a couple of 17th century poppyhead pew ends brought to Welton from Norwich by Canon Sutton of Brant Broughton.

In the sanctuary the altar is of oak and stripped of its hangings it looks like a large chest. The reredos was probably installed in 1888 and partly conceals the east windows which were installed by Rev W Williamson in 1855. The windows are memorials to Robert & Joanne Mawley of St Mary's, Aldermary, in the City of London and Thomas Mawley, son of Sarah and Edward Westhall of Croydon, Surrey. The Welton connection is as yet unknown.

The organ was installed in 1866 and was restored and improved in 1962 by Henry Willis & Sons Ltd. In 2000 the remaining restoration work on the organ was completed.