St Mary’s was built in the eleventh century, probably before or shortly after the conquest of 1066 and at least fifty years before All Saints was built. When All Saints was built in the twelfth century, St Mary’s stood to the south side of the church. The south transept of All Saints was later extended to join the north wall of St Mary’s, linking the two, with St Mary’s becoming the Lady Chapel.

By the late seventeenth century visitors to St Mary’s recorded that inside the chapel there were paintings of the Saxon kings rumoured to have been crowned here, with captions explaining that fact. However, shortly after the chapel was redundant and was being used as a timber store for All Saints.

The building collapsed in 1730. The building’s foundations had been weakened by Sexton Abram Hammerton’s grave digging. When the building collapsed the Sexton, his son and his daughter Hester had been nearby digging graves and so were trapped in the rubble. The Sexton died in the accident, but miraculously Hester and her brother were pulled from the rubble alive after seven hours. Hester had helped her father dig graves since she was 13 years old so took over his job and was a well-known person in Kingston.

The site of St Mary’s was excavated in 1926 by William Finny, antiquarian and mayor of Kingston. His archaeological digging revealed that St Mary’s Chapel had measured 60 feet by 25 feet and had flint foundations. Floor tiles found dated to 1050 earliest, and many to the thirteenth century, which shows that the chapel was being maintained and repaired. Finny believed that St Mary’s was built next to the ruins of an old Saxon church on All Saints’ site, perhaps destroyed by Viking raids in the eleventh century.