Initially the church belonged to St. Alexander Nevsky parish, but in 1882, due to the constant growth of the number of Orthodox Russians living in the city, it was made a parish church as well. From 1884 on, the church ran a parish school. The church was closed after the Germans entered to Kaunas during World War I. As soon as Lithuania regained independence, the new government confiscated all the Orthodox churches in Kaunas, regarding them as signs of intensive Russification, leaving only the smallest one - the Holy Resurrection Church - in the hands of the Russian Orthodox Church. In 1923 the church was renovated and reconsecrated by the Lithuanian Orthodox metropolitan Elevferiy (Bogojavlensky). At the same time, the church was elevated to the rank of the cathedral of Vilnius and all Lithuania Orthodox diocese, despite its small dimensions. This decision was influenced by the territorial disputes over Vilnius Region with the Second Polish Republic. Although Metropolitan Elevferiy was forced to move to Kaunas, the name of the diocese was never changed.