Nikita Khrushchev's anti-religious campaign was the last large-scale anti-religious campaign undertaken in the Soviet Union. It succeeded a comparatively tolerant period towards religion which had lasted from 1941 until the late 1950s. As a result, the church had grown in stature and membership, provoking concerns from the Soviet government. These concerns resulted in a new campaign of persecution. The official aim of anti-religious campaigns was to achieve the atheist society that communism envisioned.

Khrushchev had long held radical views regarding the abolition of religion, and this campaign resulted largely from his own leadership rather than from pressure in other parts of the Communist Party of the Soviet Union (CPSU). In 1932 he had been the First Moscow City Party Secretary and had demolished over 200 Eastern Orthodox churches including many that were significant heritage monuments to Russia's history. In July 1954, he was the initiator of the resolution of the Central Committee of the Communist Party of the Soviet Union (CPSU Central Committee) hostile to religion. He was not able to implement his ideas in practice until he achieved greater consolidation of his control in the late 1950s.

The anti-religious campaign of the Khrushchev era began in 1959, coinciding with the Twenty First Party Congress in the same year. It was carried out by mass closures of churches (reducing the number from 22,000 in 1959 to 13,008 in 1960 and to 7,873 by 1965), monasteries, and convents, as well as of the still-existing seminaries (pastoral courses would be banned in general). The campaign also included a restriction of parental rights for teaching religion to their children, a ban on the presence of children at church services (beginning in 1961 with the Baptists and then extended to the Orthodox in 1963), and a ban on administration of the Eucharist to children over the age of four. Khrushchev additionally banned all services held outside of church walls, renewed enforcement of the 1929 legislation banning pilgrimages, and recorded the personal identities of all adults requesting church baptisms, weddings or funerals. He also disallowed the ringing of church bells and services in daytime in some rural settings from May to the end of October under the pretext of field work requirements. Non-fulfillment of these regulations by clergy would lead to disallowance of state registration for them (which meant they could no longer do any pastoral work or liturgy at all, without special state permission). The state carried out forced retirement, arrests and prison sentences to clergymen who criticized atheism or the anti-religious campaign, who conducted Christian charity or who made religion popular by personal example.

Education

Khrushchev claimed that communist education intends to free consciousness from religious prejudices and superstitions.

One of the first manifestations of the campaign, as had occurred in the 1920s, was the removal of practicing believers from the teaching profession. In 1959, reports appeared 'unmasking' secret believers in faculties of education. In one case a Christian student was asked how she would teach in an atheistic school system, and she replied "I'll give all answers in accordance with Marxism. What are my personal convictions is no one's business." The same article also took concern that atheist students felt that they could not win in a discussion with believers.

The press called for more aggressively atheistic curriculum at pedagogical institutions.

In 1959 a mandatory course was introduced called 'The Foundations of Scientific Atheism' in all higher learning institutions. Evolution and the origins of life began to be taught intensively in the school system beginning in 1959–1960, and all natural sciences were subordinated to the purpose of giving students a scientific-materialistic (i.e. atheistic) attitude towards nature.

Believers could be denied graduation at institutions of higher learning on account of their religion.

The school system was criticized in a 1960 open letter to the Russian Minister of Education for failing to perform its duty to eliminate religious belief among its students. The letter claimed that believing parents were fanatics and that active believers as well as clergy were swindlers. The minister responded by outlining what the education system had been doing and reaffirming that he regarded religious belief as a very serious social epidemic.

The atheist position was not simply concerned with trying to teach a worldview without religion, but a worldview that was hostile to religion:

Anti-religious propaganda

The 21st Congress brought in a new, radical programme of anti-religious propaganda that would stay in place for the next twenty-five years.

A new anti-religious periodical appeared in 1959 called Science and Religion (Nauka i Religiia), which followed in the tradition of Bezbozhnik in aggressiveness and vulgarity, but was much less vicious.

Due to the memory among many citizens of the patriotic role that the Church had played in war with Germany, the loyalty it had shown during the war and the supportiveness of the institution in post-war peace campaigns, and the failure of the regime to rewrite history in order to remove these memories, the antireligious propaganda therefore avoided attacking the Church leadership or its institutional political reliability.

The Church's leadership also cooperated with the state's propaganda campaign by denying any persecution by the state at international peace and theological conferences, as well as to foreign press. The Orthodox hierarchy during these years largely remained unscathed by the persecution directed at the rest of the church, which the hierarchy refused to call out and which even made statements to justify.

The propaganda, unlike in the 1930s, made no promises about liquidating the Church in the near future or that the word 'God' would disappear from Russian vocabulary. There was also less artistic talent in printed antireligious cartoons and posters than there had been in the pre-war years. 'Science and Religion' even found itself having to rely on foreign atheist artists to draw their anti-religious cartoons, such as the French communist cartoonist Maurice Henry.

The propaganda, as in the 1930s, lost its originality after its enhancement in 1958 as anti-religious periodicals adopted lifeless routines in their propaganda. Every newspaper was supposed to have a plan governing their anti-religious content, but few adhered to this systematically. A number had regular columns dedicated to religion and atheism which had names such as "The Atheist Corner" or "The Militant Atheist". Very often they simply reprinted articles that had been originally printed by Pravda, TASS and other newspapers.

As in the pre-war period, lies and incitements against religion were considered permissible only if they pragmatically served the purpose of eliminating, rather than hardening, religious convictions.

Very often official policies to criticize religion without insulting believers' feelings were ignored in practice, and this widespread violation caused some to even doubt the authenticity of the policy. These attacks became even more unrestrained as a result of influence from the CPSU Central Committee. Examples of article names that appeared in this time period are: "The Howls of the Obscurantists", "The Vultures", "The Wolfish Fangs of 'God's Harmless Creatures'", "Swindlers in the guise of Holy Fathers", "A Theologian-Fomenter", and "Hysteria on the March". Believers were called "toadstools", "swindlers", "a horde", "anti-Soviet subhumans" (), "wicked enemy of all that lives", and "the rot". Secret monks were called "milksops", theologians of the True Orthodox Church were called "malignant", and Anatoly Levitin-Krasnov, historian and dissident who spoke out against the persecution, was called "Smerdiakov" (after the detestable character in The Brothers Karamazov) and a "hypocrite par excellence".

Soviet leaders saw the space programme as a tool with which to attack religion. One of the most commonly repeated antireligious arguments of this period was that the cosmonauts had not seen God when they went into space. Khrushchev claimed that Yuri Gagarin said that he did not see God when he went into orbit. Later evidence suggests that Gagarin himself was religious.

The press always accused believers of immorality, and blamed this supposed immorality on their religious beliefs. Practicing believers were libelled as lechers, demoralized weaklings, drunks, vicious criminals and parasites who did no socially useful work, just as in the pre-war period. Similarly also to the pre-war period, accusations and hate propaganda in the press often preceded arrests of clergy.

The testimony of ex-priests who denounced their former fellow clergymen for lechery, luxury, pilfering and materialistic greed, were used when available. These "confessions" often ended with appeals to still-practicing clergy to stop "fooling credulous believers" and to "stop enriching" themselves by "exploiting their ignorance".

Some, such as former professor of theology, Alexander Osipov, warned that this image was oversimplified and that religion did in fact attract intellectuals sometimes. He claimed that the Church was not a senile institution ready to fall, but had great flexibility and adaptability. He also notably criticized the atheistic propaganda for being bureaucratic routine and that atheist propagandists were often ignorant of religion (e.g. confusing Jehovah's Witnesses with Old Believers, general ignorance of Christian doctrines). Osipov also said that Science and Religion should focus on educational material since the journal was largely unread by lay believers, but that such attacks should rather occur in the general mass media.

This claim may have been incorrect, however. Believers did subscribe to Science and Religion in order to make clippings of all the quotations from Scriptures, diverse theological writings or lives of the saints, that were reprinted in the journal and criticized, as this was one of the few sources available for believers to find such material within.

Tolerant attitudes of children to believing parents or grandparents were criticized.

Pilgrims and pilgrimages were maligned in the press for charlatanism, clerical swindles to extract donations, and distraction of people from socially useful work. One of the most vicious examples of these was written by a woman named Trubnikova entitled 'Hysteria on the March' that described a pilgrimage to a spring in the village of in the diocese of Kirov, where there was supposedly an apparition of St. Nicholas centuries earlier. Trubnikova claimed that she disguised herself as a pilgrim and went with them. She claimed that they were alcoholics, hysterics, hypocrites and swindlers who faked trances and miracles (there were people who dipped themselves into the spring and then shed their crutches, which she assumed was a deceitful act). The story ended with robberies, sexual orgies and a drunken murder. Trubnikova claimed that she was rescued by a voluntary police aide in the middle of the night who claimed that these anti-Soviet sub-human Christians would have no hesitation in murdering her. She ended the article by appealing for a ban on all such pilgrimages, which were taking place right before the eyes of the Soviet public.