In 1632 the Brewhouse was hit by a fire. The extend of the damages is not known but the house was rebuilt in 1635-36. During the following years the Brewhouse developed into a fully equipped brewery with copper kettles, bottling and hop wessels, and cobbled floors.
The Brewhouse briefly regained its military significance under Sweden's siege of Copenhagen. One of the assault on Copenhagen took place at the Brewhouse in 1658-60. With its imposing walls and strategic location right by Christian IV's naval harbour that was located where the Royal Library Garden lies today, the building once again played an important part in the city's defence. The night between 7 and 8 May 1767, the Brewhouse was once again devastated by a fire and this sat an end to its life as a brewery. During the following years the building was rebuilt and then served as a depot both for the brewery guild, various public bodies and the Tøjhus Museum. Since then the house has been empty.