On 23 September 1779, during the American War of Independence, a Franco-American squadron under Captain John Paul Jones engaged two Royal Navy frigates off Flamborough Head. Jones's ship USS Bonhomme Richard, with the French frigate Pallas, took on HMS Serapis and HMS Countess of Scarborough in one of the most famous single-ship actions in naval history. Bonhomme Richard was an old converted East Indiaman, outgunned and outclassed. She locked alongside Serapis, the two ships smashing each other to pieces at point-blank range. When the British captain called for surrender, Jones is said to have shouted back that he had not yet begun to fight. Bonhomme Richard was sinking when Serapis struck her colours. Jones transferred his crew, watched his own ship go down, and sailed Serapis away. A toposcope at the lighthouse commemorates the 180th anniversary of the battle, raised in 1959.

Flamborough Head is the only chalk sea cliff in the north of England. The SSSI designation, first applied in 1952, runs from Sewerby around the headland to Reighton Sands and covers a complete sequence of Chalk Group strata. Four different chalks are named here, Ferriby, Welton, Burnham, and Flamborough. The cliffs host the only mainland British gannet colony alongside Bempton, several miles north along the coast. In autumn, when the wind swings east, birders gather below the lighthouse to watch passing seabirds, or scour the hedges for landbird migrants blown across the North Sea. The headland has its own bird observatory, dedicated to the patient business of counting and ringing what passes through.

In the nineteenth century, Flamborough's seabird colonies were under intense pressure. Boatmen were taking a hundred birds a day to sell to taxidermists, and party shooters travelled to the cliffs for sport. In 1868 Professor Alfred Newton condemned the practice in his speech to the British Association for the Advancement of Science. The local MP, Christopher Sykes, took up the cause, and the Sea Birds Preservation Act 1869 became the first Act to protect wild birds in the United Kingdom. It was a piece of Victorian conservation legislation born directly from what was happening on these chalk cliffs. Shooting continued for a while in defiance of the law, but the principle had been set, and the descendants of those nineteenth-century colonies are the gannets and guillemots still nesting on the ledges today.

A two-mile defensive ditch called Danes Dyke runs north to south across the headland, isolating five square miles of land that is naturally defended by the cliffs on three sides. The name suggests Viking origins, but excavation by Pitt-Rivers in 1879 turned up Bronze Age arrowheads, and the dyke is now understood as prehistoric. Two boat-launching beaches, North Landing and South Landing, sit within the enclosed land, and the 2016 Dad's Army film used North Landing as a location. On the north side of the headland lies Thornwick Bay, where a plaque remembers Robert Redhead, bowman of the Bridlington lifeboat, who died in 1952 trying to rescue two young girls, Joan Ellis and Gillian Fox, from drowning. The chalk towers above them where the lightning would later strike.