The manor of West Malling had been granted by King Edmund I to Burgric, Bishop of Rochester, in 946. The land was lost in the Danish Wars, then restored to the diocese in 1076. Around 1090, Bishop Gundulf of Rochester - a Norman cleric who had been a monk at the abbey of Bec in Normandy before William the Conqueror crossed the Channel - chose West Malling as the site for a Benedictine community of nuns. It was one of the very first post-Conquest monasteries for women in England. Just before his death in 1108, Gundulf appointed a French nun named Avicia as the first abbess. He endowed the new house with the manor of West Malling. Archbishop Anselm of Canterbury - the philosopher-theologian who gave us the ontological argument for God's existence - threw in the manor of East Malling. Royal charters granted the nuns the right to hold weekly markets, annual fairs, to cut wood in the king's forests, and to pasture livestock there.

As the abbey prospered, the market town around it grew. Then came the calamities. In 1190, only a century after the foundation, a fire destroyed much of the abbey and the town with it. The community rebuilt, and the rebuilt complex was the one that endured for the next three centuries. The Black Death of 1349, the most catastrophic single event in European medieval history, swept through Malling and reduced the community to four nuns and four novices - perhaps the smallest the house had ever been. They were not the only English nunnery brought to the edge of extinction by the plague, but Malling survived. The community rebuilt slowly. By 1538, immediately before the Dissolution, the abbey had an annual income of £245 - placing it in the wealthiest third of women's religious houses in England.

The last freely elected abbess was Elizabeth Rede. She had defied both Henry VIII and Thomas Cromwell over the appointment of a high steward for the abbey - an officer who handled the community's legal and estate business, and whom Cromwell wanted to be one of his own clients. Rede was deposed. In her place Cromwell installed Margaret Vernon, who had been the tutor to Cromwell's son and had already surrendered Little Marlow Priory in Buckinghamshire. Vernon's arrival was prelude to surrender. On 28 October 1538, when the Crown's agents came for the seal, they encountered the nuns' silent refusal. The buildings - the Norman church, the Early English cloister, the early 15th-century guest house, the two 16th-century gatehouses - became Crown property and then private property, passing through many families over the next three and a half centuries. Most of those owners were absentees. The buildings fell to ruin.

In the mid-18th century, a London banker named Frazer Honeywood bought the site and built a neo-Gothic mansion on it, repairing what medieval fabric still stood. Then, in 1892, the property passed to Charlotte Boyd - a remarkable Victorian woman whose stated life's work was to create a trust restoring church property to ecclesiastical use. She invited the Community of Saints Mary and Scholastica, a small Anglican Benedictine community, to settle at Malling. That community had been founded by Joseph Leycester Lyne - known as Father Ignatius of Llanthony Abbey, a flamboyant Anglo-Catholic preacher who tried to revive monasticism in the Church of England. By 1879, Mother Hilda Stewart OSB had become abbess, the first Anglican Benedictine abbess since the English Reformation more than three centuries earlier. The community left Malling in 1911 and joined the Roman Catholic Church in 1913. They live now at Curzon Park Abbey in Chester.

The community that has lived at Malling Abbey continuously since 1916 was founded in 1891 as the "Community of the Holy Comforter" - an active parish sisterhood working among the poor in Edmonton, north London. Through the preaching of Abbot Aelred Carlyle, they became attracted to the Benedictine contemplative life. In 1906 they moved to a farmhouse in Baltonsborough in Somerset to begin enclosed monastic life under Benedictine vows. In 1916, Malling's trustees invited them to take over the historic site. They have been there ever since. Little of the original 12th-century building still stands: the lower part of the tower is Norman, the upper levels Early English, with fragments of the church, a transept, and a wall of the nave attached. The refectory survives. The cloisters were re-erected in the 14th century. In 1966, the architects Maguire and Murray designed a new Grade II*-listed abbey church which the nuns use today. Since 2016, St Augustine's College of Theology - a non-residential theological college - has been based at St Benedict's Centre on the abbey grounds, training Anglican clergy on a site that has been continuously associated with women's religious life for almost a thousand years.