The monastery was originally founded at Embsay in 1120. Led by a prior, Bolton Abbey was technically a priory, despite its name. It was founded in 1154 by the Augustinian order, on the banks of the River Wharfe. The land at Bolton, as well as other resources, were given to the order by Lady Alice de Romille of Skipton Castle in 1154. In the early 14th century Scottish raiders caused the temporary abandonment of the site and serious structural damage to the priory.
The nave of the abbey church was in use as a parish church from about 1170 onwards, and survived the Dissolution of the Monasteries.
Building work was still going on at the abbey when the Dissolution of the Monasteries resulted in the termination of the priory in 1539. The east end remains in ruins. A tower, begun in 1520, was left half-standing, and its base was later given a bell-turret and converted into an entrance porch. Most of the remaining church is in the Gothic style of architecture, but more work was done in the Victorian era, including windows by August Pugin.