Peberholm is protected by strict laws. Only biologists are allowed one annual visit to the areas of the island outside of the railroad and highway to which the island owes its creation. The island is part of Natura 2000 area 142, comprising Saltholm and surrounding waters with a total area of . The same area is also under two birdprotections as habitats H110 and H126. The laws did not prevent it from being used as a border control station during the 2020 coronavirus pandemic.