On 28 October 1566 Albert I, Duke of Prussia, had the councilors Johann Funck, Matthias Horst, and Hans Schnell beheaded at the town hall's marketplace, with Johann Steinbach and Paul Skalich fleeing the country.
From 1695 to 1697 the town hall received a Baroque restyling with pilasters, bell tower, roof sculptures, and a gilded staircase with a pair of shield-holding bear statues.
In 1927 the city administration moved to the Stadthaus in northern Königsberg, with a few departments remaining in Kneiphof.
In the same year the painter Eduard Anderson advocated for the creation of the Königsberg City Museum within the town hall, which opened in 1928.
The Kneiphof Town Hall was destroyed in August 1944 during the Bombing of Königsberg in World War II.