A chapel existed in Asserton at least as early as 1291, when it was referred to as the church of Little Winterbourne. The earliest reference to a Chapel of St Mary Magdalene comes from 1349, with a further mention in 1599. Little is known about the physical nature of the church.
In 1391 the church was recorded as being a chapel within Asserton manor house, though by the mid-sixteenth century it was described as an independent building. The church was short lived compared to its contemporary in Berwick St James: its endowment was confiscated in 1547 and it was closed under the Chantries Act of 1548, around which time its silver chalice and a pair of vestments were sold. After the closure of the church, its income was for some time used to fund an Oxford Scholarship, and by 1650 the building was said to be long unused and in ruins.
The church had a rector during the thirteenth century, however by 1299 at the latest it was served instead by chaplains.