In 1664 there was a little wooden church on this site. In 1667 the church was demolished and replaced by a large wooden church with a pastor’s house and a school.  The church was consecrated in 1669. In 1670, Tsar Aleksey Mikhailovich granted the community ownership of the land with all three buildings.

The foundations for a new church, made of stone, were laid in 1964, in the presence of Peter the Great. Consecrated in 1695, the church was dedicated to Saints Peter and Paul, although it was often referred to simply as ‘The New Church’. After the fire of 1812 the church was destroyed and could not be restored. In 1817 the community bought the estate of the Lopukhin family near Pokrovka Street in Kosmodamiansky pereulok (called Starosadsky pereulok after 1922). With the financial support of King Frederick William III of Prussia and the Russian Emperor Alexander I, the newly acquired house began to be converted into a church, and a dome and cross were erected. On the 18^th of August 1819, this new building was consecrated. In February 1837 the sound of organ music could be heard in the church. The parish of Saints Peter and Paul became the largest protestant parish in Moscow, with a community which included many wealthy manufacturers, financiers and noblemen. When the congregation grew to over six thousand people, it was decided that the church should be refurbished in neo-gothic style, following designs by the architect A. A. Meinhard. The refurbishment was completed in 1862 and the following year, the bell, a gift from King William I of Prussia, was installed in the tower.

By the end of the XIX century there were 17 000 people in the community. Services were conducted not only in German, but also in Latvian and Estonian. Due to the growth of the congregation, people began to discuss the question of enlarging the church. In 1898, the decision was taken to build a church for 1700 people designed by V. A. Kossov, an architect and academician who had also collaborated on the planning of the Cathedral of Christ the Saviour. In May 1915 anti-German riots swept through Moscow, taking the lives of many in the community and causing significant damage to the church. In November 1936 Pastor Alexander Shtrek was arrested together with the church staff and shot dead; further church services were stopped and the community ceased to exist. On  the17^th July 1938, by the common ordinance of Moscow City Council (Mossovet) and Moscow Regional Executive Committee (Mosoblispolkom), the building was given to Krasnogvardeysky district council (Krasnogvardeysky raisovet) to serve as a cinema.  The cathedral was subsequently given to ‘Diafilm’ studio, which redesigned the building. The Evangelic-Lutheran Church in Russia never closed down officially, but in the wake of repression, it effectively ceased to exist by the end of 1938. Fifty years later, in 1988, the church was reconstructed under the guidance of Bishop Harald Kalnins. In May 1991 an initiative group submitted a registration application to the Department of Justice of Moscow City Council. Then, on the 7th of June 1992, Moscow City Government passed a resolution handing the cathedral back to the Lutherans, and in the same year, building work was begun.