The church went up in the thirteenth century — around 1250 by the usual reckoning, though some Danish accounts put it half a century earlier — in the late Romanesque style, a plain brick structure of nave and choir like a hundred other Jutland village churches. It had arched pilasters, some of which survived to the end. A tower stood here in the eighteenth century; it was pulled down and replaced by a free-standing wooden bell tower. Crucially, it was built in the middle of its parish, about a kilometre from the coast. That was a sensible distance in 1250. It stopped being one somewhere in the intervening centuries, and by 1926 the parish had built a new church at Lønstrup and moved on. The National Museum of Denmark took the old building into its care in 1952.

On 6 December 1808, during the Napoleonic Wars, the British frigate HMS Crescent was carrying supplies to the Royal Navy at Gothenburg when she went down off this coast. Seven officers and fifty-five seamen came ashore alive. More than two hundred men did not, and they were buried together in a single grave in Mårup's churchyard — sailors from a country Denmark was then at war with, given ground by the parish that found them. Two more British ships were lost on the Danish west coast in the same period, and in 1895 the British installed a memorial tablet naming the dead of the Crescent, the St George and the Defence. The frigate's anchor was set beside the church, where it stayed for more than a century: an object heavy enough that even the sea took its time.

Storms through the late twentieth century and into the early twenty-first tore at the cliff and damaged one corner of the building. By the middle of the 2000s the sea was nine metres away. What followed was a genuinely bitter national argument — let nature take its course, or spend public money fighting a coastline that had been losing for three hundred years. Danish firms tried coastal protection. Nothing held. In August 2007, after four years of debate, the National Museum decided to move the church to an open-air museum, then found the cost prohibitive and local feeling strongly against it. At the end of November 2007 the culture and land-protection authorities settled on the other answer: dismantle it, gradually, in place. The last service was held on Easter Monday, 24 March 2008.

In the autumn of 2008 the roof and the interior came off and went into storage. The walls were left standing, which meant that for three more years there was still a church-shaped ruin on the cliff. In autumn 2011 the western wall was taken down, leaving three walls and an open view to the water. Erosion in the summer and autumn of 2012 pulled large sections of ground away north and south of the site, and by that November what remained stood nine metres from the edge again. Work continued in stages until 18 September 2015, when the last foundation stone was lifted. By May 2016 the church was gone and the anchor had been moved inland, away from the cliff. The materials sit in storage at Hjørring on the chance that money for a reconstruction ever appears. In the final clearing, archaeologists found a child's grave beneath the altar — a placement usually reserved for families of standing, and an unlikely last discovery on a site everyone assumed was finished.

The graveyard is still there, and the anchor, and the tablet. At its peak the site drew around 300,000 visitors a year, most of them Danish, some of them coming specifically because Gabriel Axel filmed Babette's Feast here in 1987 — the story is set in Norway, but Axel wanted this landscape, and the film went on to become the first Danish production to win the Academy Award for Best Foreign Language Film. The same coast keeps making the same decision. In 2019, less than two kilometres down the cliff to the south, Rubjerg Knude Lighthouse was rolled bodily inland on rails to buy it a few more decades. And Mårup has a distant relative in Pomerania: the church at Trzęsacz, which nobody dismantled, and which largely collapsed into the Baltic in 1901.