The present abbey church dates mainly from c.1150 although there was further work on it in the 14th century. The spire was supposed to be between 23 and 45 feet higher than that of Salisbury Cathedral but it fell in 1479, demolishing the eastern end of the church. Nothing was done to replace this but a temporary wall was erected at the eastern end of the nave; it is still there. After the dissolution of monasteries in 1539 William Stumpe bought the abbey and later, as the parish church of St. Paul was in a poor state, gave the abbey church to the town for their parish church. A license to use it as such was granted in 1541. Around 1660 the west tower of the abbey collapsed resulting in the nave being shortened by two bays and a new wall erected. This nave was used as the parish church.
By 1822 restoration work was required and later in the century, in 1875, gas lighting was installed. By the early 20th century parts of the building had become dangerous and further restoration was carried out by Harold Brakspear. This included repairing two ruined bays at the western end and building a spiral staircase and a roof walkway. The work was completed in 1912. In 1927 Brakspear carried out more restoration work and on December 6th 1928 a service was held to re-hallow the abbey.
In 1946 the vicarages and parishes of Malmesbury and Westport were united under the name of Malmesbury with Westport St. Mary. The Cloister Garden, to the north of the abbey was created in 1980 and in 1984 the new parish od Brokenborough was added. The church is in the Diocese of Bristol and the registers from 1590 (marriages) and 1591 (christenings and burials), other than those in current use, are deposited in the Wiltshire and Swindon Record Office. Malmesbury is one of few towns, Tewkesbury is another local example, in having a former monastic church as its parish church.