According to a popular legend, the first wooden Orthodox chapel located on the place of today's St. Nicholas church was built around 1340.
However, in 1350, Uliana of Tver, the second wife of prince Algirdas, ordered to build a new brick church.
In 1839, the Russian local government closed the Uniate parish and given the building back to the Orthodox.
After the failed Polish January Uprising, it was completely rebuilt in Neo-Byzantine style on the personal initiative of general-governor of Vilnius Mikhail Nikolayevich Muravyov-Vilensky.
Muraviev ordered also the construction of St. Michael the Archangel chapel which was to commemorate his victory over the Polish uprising.