By 1941, the persecution of the Church throughout the country was suspended. At the same time, Marx’s statement that “religion is the sigh of an oppressed creature, the soul of a heartless world, the spirit of soulless timelessness. It is the opium of the people,” remained one of the main attitudes of the atheistic state. In 1938 in the USSR there was not a single monastery, and the number of Orthodox parishes, according to various estimates, ranged from 150 to 400. By 1941, the Russian Orthodox Church already had 64 monasteries (in 1914 there were 1025 of them) and over 3 thousand. active temples, more than 90% of the churches were located in the territories incorporated into the Soviet Union in 1939-1940. The government could not ignore the new masses of the Orthodox population and was forced to create the appearance of religious tolerance.

On the first day of the war, June 22, the Locum Tenens, Metropolitan Sergius, despite his physical shortcomings — deafness and lack of mobility, wrote and personally typed a message in which he called on the Orthodox Russian people to defend the Fatherland. In the message, which Sergius was able to send to all corners of the country, it was noted: "Fascist robbers attacked our homeland. The times of Batu, the German knights, Charles of Sweden and Napoleon are repeated. The miserable descendants of the enemies of Orthodox Christianity want to try our people again kneel before untruth. " Metropolitan Sergius called on everyone to remember the holy leaders of Russia Alexander Nevsky, Dmitry Donskoy and bless the people to defend the country's borders, emphasizing that "the Lord grants us victory." The document certainly was historical. However, the position of the ROC turned out to be incomprehensible to many abroad, where they believed that the outbreak of war should exacerbate the contradictions between the state and the Church to the limit.

Following Sergius on July 26, 1941, Metropolitan Alexy addressed the believers of the Leningrad diocese with the message “The Church Calls for the Defense of the Motherland”. Thus, in extraordinary circumstances, the Church’s predestination was not prejudice and offense, but the centuries-old traditions of the national and patriotic service of Russian Orthodoxy. During the war years, the patriarchal locum tenens addressed the believers with patriotic appeals 24 times, responding to all the major events in the country's military life.

The danger looming over the USSR, the need for national unity for victory over the enemy, the patriotic position of the Russian Orthodox Church prompted the Soviet government to change its religious policy. The country began to open parishes, closed in the 30s, the surviving priests were discharged from the camps and resumed service in the temples. The anti-religious campaign ceased in print, the Magazines published by the Union of Militant Atheists ceased to go beyond the shortage of paper, and the Union itself ceased to exist without an official dissolution.

In the conditions of danger looming over Moscow in 1941, Metropolitan Sergius was evacuated to Ulyanovsk, which became a kind of spiritual center of Russia. It was from Ulyanovsk that Sergius sent his messages around the country and denounced the invaders for spilling innocent blood, ruining and scolding national shrines.

The patriotic activity of the ROC was manifested in the war years in various forms. Thus, services continued in 5 active Orthodox churches of Leningrad even during the blockade. Mi-tropoly Alexy remained in the city and served every Sunday in St. Nicholas Cathedral, calling on the people for courage and hope. Prayers for the victory of the Red Army were held throughout the country. Hundreds of clerics were in the ranks of the army. The future patriarch of Moscow and all Russian Pi-Pimen began his combat career along the fronts of the Great Patriotic War as a deputy company commander. In Krasnoyarsk, Archbishop Luka (Voyno-Yasenetsky), a prominent medical scientist who was awarded the State Prize of I degree in 1946, worked as the chief surgeon of the evacuation hospital. Evidence of the recognition of the merit of the clergy by the state was the appointment of the Metropolitan of Kiev Nicholas as a member of the Emergency Commission for the establishment and investigation of the atrocities of the Germans and their accomplices.

One of the most important areas of patriotic service to the Church during the war was material assistance to the state and the army. The collection of donations to the defense fund and the Soviet Red Cross began on June 23, 1941. Only in the Leningrad diocese over 6 million rubles were raised, in the Vologda region - 2.5 million rubles, in the Krasnoyarsk Territory - 4 million rubles, in the Stavropol region 6 million rubles, and in the Gorky region - more than 9 million rubles. In all, during the war years, contributions from the ROC to the defense fund amounted to over 300 million rubles. Moreover, the funds were donated even in the territory occupied by the enemy and from there were delivered to the People's Commissariat of Finance of the USSR. It is known that Fyodor Puzanov, a resident of the village of Bro-Dovichi in the Pskov region, collected among the believers gold, silver, church utensils and money in the amount of 500 thousand rubles, and then through the partisans handed them over to the mainland.

The funds of the ROC created military units. At the call of Metropolitan Sergius, on December 30, 1942, the creation of a tank column named after Dmitry Donskoy began. On March 7, 1944, 40 T-34 tanks were transferred to units of the active army. In Novosibirsk , funds were raised for the construction of the Siberian squadron "For the Motherland"; the formation of the Alexander Nevsky aviation squadron was going on.

At the turn of 1942-1943. Metropolitan Sergius took an important step towards the de facto legalization of the Church. He sent a telegram to Stalin asking for permission to open a bank account of the Russian Orthodox Church, which would contribute funds donated for defense in all the churches of the country. At the beginning of 1943, Stalin gave his written consent to this and, on behalf of the Red Army, thanked the Church for its work. Having received permission to open a bank account, the ROC became a legal entity.

On August 31, 1943, Metropolitan Sergius returned from Ulyanovsk to Moscow. On September 4, he, along with Metropolitan Alexy and Nikolai, was invited to the Kremlin to talk with the chairman of Sovnarkko-ma Stalin. During the meeting, several important goals were achieved. Already on September 8, the Council of Hierarchs of the Russian Orthodox Church was to open its work, the main task of which was to elect a patriarch. In addition, a special state body was created to ensure communication between the government and the leadership of the Church - the Council for the Affairs of the Russian Orthodox Church. The government also decided to provide the ROC to house the patriarchate for the former residence of the German ambassador to Moscow, Schulenburg. It was decided to open in Moscow the Theological Institute and the Theological and Pastoral courses.

On September 8, 1943, carrying out Stalin’s wish to prepare the Council in the "Bolshevik tempo", 19 hierarchs of the Russian Orthodox Church gathered in Moscow. The primacy of the Council was the election of a patriarch. The voting was unanimous, and Metropolitan Sergius was elected to the patriarchal throne, which has actually fulfilled these duties for 17 years. Sergius Patriarchate, however, was not long. He died on May 15, 1944. During the meetings of the Local Council of the Russian Orthodox Church, held from January 31 to February 2, 1945, Alexy I became the thirteenth patriarch of Moscow and All Russia (in the world Sergey Vladimirovich Simansky). At the same time, the Council adopted the Regulation on the Administration of the Russian Orthodox Church, which was in effect until 1988.

In the course of the Great Patriotic War, church construction spontaneously developed in the occupied territories of the USSR — the surviving temples were repaired, opened and consecrated, prayer houses were erected. In the religious policy, the Nazis, therefore, were guided by directives that allowed for the revival of local church life, but hindered the creation of nationwide church administrative structures. Hitler considered it necessary to avoid a provision in which one church would satisfy the religious needs of large areas. More than that, it seemed desirable to turn almost every village into an independent sect: "If, as a result, some villages want to practice black magic, as Negroes or Indians do, we should not do anything to prevent them."

The German policy on the ROC was aimed at encouraging any form of split and separation. Over the years of the war, on the territory under the occupation of the enemy, 7.5 thousand churches and about 40 monasteries were opened. But despite this, the German authorities did not succeed in achieving a separation of the people. Contrary to the expectations of the Nazis, the churches did not become the focus of anti-Soviet propaganda. On the contrary, they sought to assist the poor, prisoners of war, becoming guardians of national traditions for a significant part of the population of the occupied territories.

The position of the overwhelming majority of the ministers of the ROC was reflected not by those who prayed for Hitler, but by those who strengthened the spirit of the population and helped the state to stand in the fight against the enemy. By the end of the war, the basic principles of the new religious policy of the Soviet government were formed, characterized by great tolerance towards Orthodoxy. Only from January to November 1944 over 200 churches were opened throughout the country.

In August 1945, 10,243 churches and prayer houses operated in the USSR, there were 75 Orthodox monasteries (29 of them were opened during the German occupation). The Council of People's Commissars of the USSR suggested that local authorities should not interfere with their activities, retaining their occupied residential and office premises, land, livestock and agricultural implements. A government decree of August 23, 1945 was allowed to make church bells in cities and villages. All this testified both to a certain increase in religious sentiments in the mass of the population, and to the recognition by the state of the merits of the Church during the war years.