Sitting directly under the Norman church, the archaeologists discovered a square formed from flint walls, surrounded by a circular ditch.
A small number of burials found nearby suggest the site once served as a Saxon church.
Although small in footprint, the church would have been fairly tall and reminiscent of St Peter’s, a standing Saxon Church in Barton-upon-Humber.
Dr Rachel Wood, lead archaeologist for Fusion JV, said: “This is a fantastic discovery that we are all very excited to excavate.
“The work undertaken at Old St Mary’s is a unique archaeological opportunity to excavate a medieval parish church with over 900 years of meaning to the local community.