The church later came under the jurisdiction of the bishop of Worcester and supported financially by the local aristocracy or thanes. From the name of one of these thanes "Wagen" derives the second part of the name of the village (Wawen). His name is also linked to the foundation of Leofric's monastery in Coventry dating back to the early 11th century.

The original church was dedicated to St Mary and only much later dedicated to St Peter-in-Chains a century or so after the Norman invasion of 1066. At this time the church was significantly enlarged with a new nave, chancel and transept to accommodate the increasing numbers in the congregation. After the Norman conquest the church came under the jurisdiction of the French Benedictines who built a priory on the site of the present day church field. One of the priors of Wootton Priory Peter de Altaribus rebelled in 1281, refused to carry out his duties and was excommunicated; another Prior, Michael de la Bouche died of the Black Death in 1350.

As enmity between England and France increased, culminating in the Hundred Years' War in 1338, the French monks were often the target of local dissatisfaction and for a time the Priory came under the jurisdiction of the Carthusians in Coventry. However, in 1443, Henry VI had it closed down and the Priory fell into ruins. In 1447 the Church came under the patronage of King's College, Cambridge.