The Prussian Confederation, consisting of the gentry and burghers of western Prussia, rises up against the Order in 1454, beginning the Thirteen Years' War.

Much of Prussia is devastated in the war, during the course of which the Order returns Neumark to Brandenburg in 1455.

In the Second Peace of Thorn (1466), the defeated Order recognizes the Polish crown's rights over western Prussia (subsequently Royal Prussia) while retaining eastern Prussia under nominal Polish overlordship.

Because Marienburg Castle is handed over to mercenaries in lieu of their pay, the Order moves its base to Königsberg in Sambia.