The global population of Cape Gannets has decreased by over 20% in just three generations! This is largely as a result of overfishing in the small pelagic fisheries of the South African and Namibian coastlines. Other threats to the species include oil pollution, climate change (that brings increased risk to diseases) and predation from seals. With a reduction of food availability, Cape Gannets have taken to scavenging at the back of fishing trawlers, taking fish as the large purse-sein nets are pulled to the surface. They also feed on offal that is dumped overboard. This offal is less nutritious than there normal prey and as a result breeding success at colonies is being reduced.

The species breed on offshore islands in Namibia, the Western Cape and in Algoa Bay off Port Elizabeth. Annual counts on these islands are indicating that there is a decline in numbers off the Namibian and Western Cape islands and Bird Island is now the species global stronghold. These islands lie on major shipping routes and in the case of Malgas Island in Saldahna Bay and Bird Island in Algoa Bay, huge tankers regularly pass close to the islands placing them at great risk to an oil spill.

Conservation efforts are currently focused on proclaiming a marine protected area within Algoa Bay and in proclaiming a MPA on the west coast that would help protect feeding grounds for this species. These MPAs will also help in the conservation of many marine bird, mammal and fish species and would also protect crucial habitats.