The manor was held by the King in 1086, previously by Edward the Confessor. The Domesday Survey also mentions a church and three hides attached to it, held by two clerics who pay tax with the County. This argues a degree of independence from the manor which was to have far-reaching consequences.
In 1125 the manor was transferred to Henry I's new foundation at Reading, but Bishop Roger of Salisbury (1107-39) retained the church and its revenues. On Roger's death, Empress Matilda gave the church to the monks of Reading by charter, confirming their possession of the manor at the same time. The gift of the church was confirmed by Henry II when Roger of Salisbury's successor, Bishop Joceline (1142-84) tried to claim it.
Successive bishops were concerned to retain an interest in the church. By an agreement between Hubert FitzWalter (Bishop of Salisbury 1189-93) and Abbot Hugh of Reading, the revenues of Thatcham and Bucklebury were assigned to Abbot Hugh's hospital in Reading, saving only sufficient provision for vicars. This arrangement was confirmed by Clement III (1187-91) and by Celestine III (1191-98), and would seem to uphold the abbey's claims over the bishops', however a papal act of 1206 indicates that the two were again in dispute over Thatcham and Bucklebury. In 1240 the then bishop, Robert Bingham, ordered that the rector (Gilbert de Biham) and his successors should pay 20 marks annually to the abbey in exchange for the church an arrangement which effectively returned the church to the diocese. It was not until 1309 that, after a petition by Queen Isabella, Pope Clement V ordered that Thatcham church be restored to the abbey on the death or cession of the rector. A licence by Edward II dated 1310 allowing the abbey to appropriate the church in mortmain indicates that they did not have long to wait.