The Russian mission in Munich, the capital of Bavaria, was opened in 1798. However, since there was no domestic church, Orthodox diplomats attended the Greek Trinity Church on Salvatorplatz, where services were held for all Orthodox residents of the city. On major holidays, some prayers were read in Russian. Emperor Nicholas I provided financial support to this church to care for his subjects.

The Russian parish in Munich appeared after the Bolshevik revolution, when 200-300 emigrants from Russia settled in the city. In 1921, irregular services began in rented premises, where the iconostasis from the Nikolskaya church at the villa of the Counts Adlerberg on Tegernsee was used. In 1922, a community was established, led by priest Nikolai von Ber in 1923 and 1927. Services were held in the "Matildenshtift" hall, and the community was called Nikolskaya.

From the late 1920s, the parish, subordinate to the Russian Orthodox Church Outside Russia (ROCOR), faced difficulties due to the lack of a permanent priest, and services were conducted only on major holidays by invited priests. In 1937, the situation improved when Fr. Andrei Lovchiy, the future Archbishop of Berlin and Germany, was appointed a traveling priest for Bavaria and served the community until his death in 1971.

From 1940, the number of parishioners began to grow due to new refugees and "Ostarbeiters" from Russia. After Easter 1941, the community moved to a temporary barrack church at Denningersstraße 5, where they opened a parish school and a catechetical circle. During the war, there were difficulties in providing candles, church wine, and flour for prosphora. Despite this, Igumen Alexander (Lovchiy) began publishing the parish "Sunday Leaflet" in 1941. A missionary committee was established to work with prisoners of war and "Ostarbeiters."

Until 1949, the parish maintained the barrack church, but two years earlier moved to a large hall on the first floor of the music school on Salvatorplatz, where before the war there had been an American chapel and library. The school was adjacent to the Greek Trinity Church, which the Russian clergy temporarily used from May 1943 to February 1946. In 1945, 2000 people participated in the Easter procession around it.

In the post-war years, Munich became a center for Russian church emigration. Here, the episcopal assemblies of ROCOR were held, and the administration of the German diocese was established. In this regard, the Nikolskaya church received the status of a cathedral in 1952. By the early 1950s, there were 30-40 thousand displaced persons from Russia in Munich and its surroundings, who created 25 parishes served by 30-40 emigrant priests. However, in the 1950s and 1960s, many camp churches closed due to the departure of parishioners and clergy, and the Holy Nicholas Cathedral gained special significance in Bavaria.

The church on Salvatorplatz was consecrated on May 22, 1947, by Metropolitans Anastasy and Seraphim (Lyade), Bishop Alexander (Lovchiy), and ten priests. The iconostasis and church utensils were transported from the previous church. The church was considered temporary, and since 1957, city authorities constantly demanded its relocation, but all proposed options were unsuitable.

In the 1980s, architect Georgy A. Remmikh developed a project for a single-altar church in the Novgorod-Pskov style. A model was displayed in the cathedral, and fundraising began for the purchase of a land plot. The building was planned to be erected in the suburb of Munich, Laim, but German authorities constantly delayed the matter, citing the height of the church and local residents' dissatisfaction with the ringing of the bells. Fundraising was slow. The parish consisted of about three thousand believers, mostly elderly people, assimilated Russians, or converted Germans who did not understand the liturgical language.

After 1991, there was a sharp increase in the influx of new Russian emigrants to Munich, many of whom embraced Orthodoxy. The active church became cramped. At the end of 1992, the Russian community was given an American prayer house on the outskirts, in a former military town. The move to the new building in the Perlacher Forst area took place two years later, before Trinity. The altar and iconostasis were transferred from Salvatorplatz. The cathedral received a new name, in honor of the Holy New Martyrs and Confessors of Russia.

After the move, the building was remodeled in the Orthodox style under the guidance of the starosta V. A. Yesikovsky, who was awarded a blessed certificate. In 1995, a left chapel of St. Nicholas with a dome was arranged. The oak iconostasis for it was carved in the Baltic States. The church was consecrated on March 3, 1997, and the chapel on May 19, 2005. Services are held there in winter, on weekdays, and on non-12 major feasts.

The remodeling affected all parts of the building. The side facades were decorated with blind arcading, preserving narrow semi-circular windows with colored glass. The eastern apse is decorated with arches with two windows and a relief cross. A one-story parish hall with a separate entrance was added to the south.

On April 27, 2000, the construction of a bell tower in the Pskov style began in the western part of the church. On May 1 of the same year, a stone from Jerusalem and a vessel with a church-building certificate were placed in its wall. On the Feast of the Exaltation, a permanent cross was installed above the entrance. On December 1, 2002, bells cast in the workshop of the Shuvalov brothers in Tutayev were raised to the bell tower. The two-tiered bell tower, the most Russian part of the exterior, rises above the porch with a small dome.

Inside, the building is elongated in plan and has a gabled roof. Spacious choirs are located above the entrance. The interior is illuminated by three-tiered crystal chandeliers. Icons are hung on the whitewashed walls. The two-tiered iconostasis was made in Russia, but the icons were taken from the old iconostasis. Additional images were painted by local iconographer Tamara Sikoeva. The new church still lacks the atmosphere of prayer and Orthodoxy; it seems too large and poor in decoration.