The city became mostly Protestant in the 16th century during the Protestant Reformation.During the time of burgomaster Henry Stroband (1586-1609) the city became centralised and power went into the hands of city council. At the same time Catholics became persecuted and discriminated as city officials of Protestant faith tried to block the influx of Catholic population into the city and harassed Jesuits located in the Church of Saint John (Kościół Świętego Jana). In 1724 Lutherans plundered the Jesuit collegium which led to Polish Royal court sentencing the burgomaster Johann Gottfried Roessner and some other citizens of Lutheran faith to death penalty [1].

In 1793 the city was forcefully annexed by the Kingdom of Prussia in the Second Partition of Poland. In 1807 Toruń became part of the Duchy of Warsaw created by Napoleon Bonaparte, although it was returned to Prussia upon his defeat in 1814. French people prisoners of war taken during the Franco-Prussian War built a chain of forts surrounding the town in 1870. The following year Toruń, along with the rest of Prussia, became part of the German Empire.

In the Treaty of Versailles in 1919 after World War I, Toruń returned to Poland 147 years after being partitioned and became the capital of the Pomeranian Voivodship. The Baltic Institute was established in the city in 1925 with the task of documenting Polish heritage in Pomerania. Toruń was occupied by Nazi Germany after the Polish September Campaign in 1939 and administered as part of Danzig-West Prussia. During World War II, the chain of forts were used by the Germans as POW camps collectively known as Stalag XX-A. Toruń was liberated from Nazi occupation in 1945.