The town was built in Prussia around the fortress Ordensburg Marienburg, which was founded in 1274 on the east bank of the river Nogat by the Teutonic Knights.

During the Thirteen Years' War, the castle of Marienburg was pawned by the Teutonic Order to their soldiers from Bohemia.

The river Nogat and flat terrain allowed easy access for barges a hundred kilometers from the sea.

During Prussia's government by the Teutonic Knights, the Order collected tolls on river traffic and imposed a monopoly on the amber trade.

But when the Poles finally took control, Blume was hanged and quartered, and fourteen officers and three remaining Teutonic knights were thrown into dungeons, where they met a miserable end.

[5] In the early 19th century, Prussian authorities acknowledged the town's Polish-speaking community, ensuring that priests could deliver the sermon in Polish.

[5] Under the terms of the Treaty of Versailles after World War I, the inhabitants were asked in a plebiscite on 11 July 1920 whether they wanted to remain in Germany or join the newly re-established Poland.

During the Weimar era, Marienburg was located at the tripoint between Poland, Germany and the Free City of Danzig.

[12] After the German invasion of Poland in September 1939, leaders of the Polish minority were arrested and sent to concentration camps.

[15] The Polish resistance was present in the town and would smuggle underground Polish press[16] and data on German concentration camps and prisons, and organize transports of POWs who escaped the Stalag XX-B to the port city of Gdynia, from where they were further evacuated by sea to neutral Sweden.

[17] Near the end of World War II, the city was declared a fortress and most of the civilian population fled or were evacuated, with some 4,000 people opting to remain.

In early 1945, Marienburg was the scene of fierce battles by the Nazis against the Red Army and was almost completely destroyed.

[19] In October 2008, during excavations for the foundation of a new hotel in Malbork, a mass grave was found containing the remains of 2,116 people.

A Polish investigation concluded that the bodies, along with the remains of some dead animals, may have been buried to prevent the spread of typhus, which was extant in the turmoil at the end of World War II.

[21][22] After World War II, the town was gradually repopulated by Poles, many expelled from Polish areas annexed by the Soviet Union.

[5] In the following years, most of the war damage was removed, and in 1947 the railway bridge on the Nogat was rebuilt, after it was destroyed by the Germans in March 1945.

[5] Also following the war, the Old Town in Malbork was not rebuilt; instead the bricks from its ruins were used to rebuild the oldest sections of Warsaw and Gdańsk.