Lancaster Priory's founding charter dates to 1094 when Roger of Poitou listed it as a gift to the monastery of St Martin of Séez in Normandy. However, it is likely that Christian worship had been present on the site prior to this date, based on early medieval fragments of stone and coins found on the site.
The Priory was a small community of Benedictine monks, under priors two of which at least were sent from Séez. It is thought that claustral buildings lay to the north of the church, but there is no trace of them above ground and they have not been investigated archaeologically.
St Mary's became the parish church for Lancaster in 1430, under the oversight of the Bridgettine Convent of Syon, following Henry V's suppression of monastic houses in the ownership of French abbeys. Following the transfer, the church was extensively rebuilt. The incumbent from 1466-1484, Richard Burton, was also clerk of works at Eton College. As a parish church, it survived the disolution of Syon at the Reformation.