The first Christians arrived in the 5th century, fleeing persecution. Around 516 the Welsh king Einion Frenin invited the Breton saint Cadfan to leave his first community at Tywyn and move to the island. Under Cadfan's leadership, St Mary's Abbey was built. The community grew. By the early Middle Ages, Bardsey was a major pilgrimage destination - bards called it 'the land of indulgences, absolution and pardon, the road to Heaven and the gate to Paradise.' The tradition that 20,000 saints are buried here is more poetic than literal, but it is also probably an undercount of the actual graves; for nearly a millennium, monks and pilgrims and dying believers had themselves carried to the island so they could rest beneath its soil. In 1188 the abbey was still a local Celtic institution. By 1212 it had been brought into the Augustinian order. In 1535 the Suppression of Religious Houses Act, ordered by Henry VIII, dissolved it; the buildings were demolished in 1537. The choir stalls and bells went to Llanengan on the mainland. A Celtic cross stands today among the abbey's ruined bell tower, commemorating the dead.

It became tradition in the 19th century for the islanders to elect a king. The first known title-holder was John Williams. Beginning in 1820, each new king was crowned by Baron Newborough or his representative, with a tin crown brought across from the mainland. The third recorded king, John Williams II, was deposed in 1900 - asked to leave the island because he had become an alcoholic. The last king was Love Pritchard. When the First World War broke out in 1914, Pritchard offered himself and the men of the island for military service. He was seventy-one and was refused. In response, he declared Bardsey a neutral power. The Newborough estate sold the crown to the Merseyside Maritime Museum in Liverpool in 1986, against Pritchard's wishes that it remain in Wales. It is now on loan to Storiel gallery in Bangor.

Sometime in the late 1990s, a man called Ian Sturrock noticed a gnarled and twisted apple tree growing by the side of one of the cottages, Plas Bach. In 1998 the National Fruit Collection at Brogdale - the home institution for British apple expertise - examined a specimen and concluded the tree was unique. It was a previously unrecorded cultivar, an apple variety found nowhere else in the world. The thinking is that it is a survivor of an orchard the monks tended a thousand years ago - the last living member of an orchard that was old in the medieval period. The Bardsey Apple is now commercially available, propagated by grafting, and its discovery led to a wider revival of interest in lost Welsh apple varieties. There is something quietly wonderful about an apple tree that survived for ten centuries on a small windswept island, unnoticed, until a man with a sharp eye walked past it.

Bardsey Island Trust bought the island in 1979 from the Newborough estate. When the trust advertised in 2000 for a tenant for the 440-acre sheep farm, they received 1,100 applications. The tenancy went to the Royal Society for the Protection of Birds, which managed the land for habitat as well as production - oats, turnips, swedes, geese, ducks, chickens, sheep, Welsh Black cattle - until the RSPB withdrew at the end of its term. The island is now home to the Manx shearwater colony, between 26,000 and 30,000 pairs that come ashore each year under cover of darkness to nest in abandoned rabbit burrows. Grey seals haul out on the rocks in numbers - more than 200 in mid-summer, with about 60 pups born each autumn. Bottlenose and Risso's dolphins, harbour porpoises, even minke whales pass through the food-rich currents around the island. The Bardsey Bird and Field Observatory has been counting and ringing migratory birds since 1953. And as of 2025, three people live on the island year-round. The next tenant of the sheep farm has been sought, again, by BBC News. The wind, the saints, the apple tree, the shearwaters, and now barely anyone to watch them.