The National Trust owns Lundy and the Landmark Trust manage it under lease. English Nature supports the Landmark Trust in employing a warden for the island. Lundy has three main conservation priorities, the endemic Lundy cabbage and its two associated beetles; its breeding seabirds; and its heathland.

The Lundy cabbage and its beetles are vulnerable to suppression by introduced rhododendron and to grazing by rabbits, sheep and goats. Rhododendron has spread on the steep cliffs which the cabbage uses as a refuge from grazing, as well as the adjacent slopes, and leading to the loss of important vegetation, including Lundy cabbage. Where it poses a threat to the Lundy cabbage, it is controlled and cleared to maintain the open cliffs and slopes. In addition, fencing excludes large grazing animals from some areas to prevent problems from their grazing but overgrazing by rabbits remains a major problem for the plant.

A partnership of English Nature, the Landmark Trust, the National Trust and RSPB is working together on the Lundy Seabird Recovery Project. This project aims to protect the breeding grounds of the puffins and Manx shearwaters on Lundy. Rats eat the eggs and chicks of burrow-nesting birds. It is believed that, on Lundy, this has pushed the numbers of puffins and Manx shearwaters to the point where they may be lost from the island altogether. In 2001 work began to remove rats from the island, using specially designed bait stations. Monitoring is continuing to assess how the project is progressing.

The heathland on Lundy is vulnerable to overgrazing, which can affect the quality of the habitat and cause erosion. There is a managed grazing stock on the island but the semi-wild goats, Soay sheep, deer and rabbits are more difficult to control. A management plan is in place to protect the heathland, by promoting a balanced approach to grazing. English Nature and the Landmark Trust regularly review the grazing scheme on the island.