The castle suffered a terrible siege during the war between Isabella the Catholic and her niece Juana la Beltraneja. The city defended the cause of Isabella and the castle that of Juana.
During the Modern Age it lost its old defensive function, so in the 16th century a gunpowder factory was established there and the first training school for artillerymen in Spain.
A fire that occurred in 1736 led to the destruction of the interior.
During the Peninsular War the French transformed the enclosure and they built a modern fortress, but when they left Burgos in 1813, after the war was lost, they blew it up. The castle explosion caused enormous damage to the old town.