It served as a prison into the late 1930s, especially the dreaded Tenth Pavilion of the Warsaw Citadel (X Pawilon Cytadeli Warszawskiej); the latter has been a museum since 1963.

The cornerstone was laid by Field Marshal Ivan Paskevich, de facto viceroy of Congress Poland.

The list of Poles imprisoned and/or executed there up through World War I includes many notable patriots and revolutionaries: Apollo Korzeniowski, writer, political activist and father of Joseph Conrad; Romuald Traugutt, leader of the 1863 January Uprising; Jarosław Dąbrowski, later military chief of the 1871 Paris Commune; Feliks Dzierżyński, a leader of the Russian Revolution of 1917 and founder of the Cheka secret police; the Marxist theoretician and revolutionary, Róża Luksemburg; the future Marshal of Poland, Józef Piłsudski; Piłsudski's political archrival, Roman Dmowski; and Eligiusz Niewiadomski, assassin of Poland's first president, Gabriel Narutowicz.

In 1915 Warsaw was occupied by German forces with little opposition from the Russian garrison, which abandoned the fortress and withdrew east.

During the 1944 Warsaw Uprising, the Citadel's German garrison prevented linking between the city center and the northern Żoliborz district.