A wooden church stood on the site of the current cathedral since 1565. The history of the new temple is linked to Peter I, who visited Kazan from May 27 to 30, 1722, during his Persian campaign. This was his third visit to the city; the first took place in 1695 during the Azov campaign, and the second in 1708 when the admiralty opened in Kazan. The emperor stayed with the famous merchant and philanthropist Ivan Afanasyevich Mikhlayev, whose two-story brick house was located next to the wooden Peter and Paul Church. On May 30, Peter I celebrated his 50th birthday in Kazan. In honor of this event and in gratitude for the trust of the sovereign, who entrusted him with the management of loss-making state manufactories, Mikhlayev decided to build a new stone cathedral in the name of Saints Peter and Paul, which was to become the tallest and most luxurious in Kazan and the Volga region.

The construction of the temple was carried out by local craftsmen over four years. They based it on a standard plan for a town church, but did not take into account that the traditional scheme does not allow for significant height, and as a result, the vault collapsed. Upon learning of this, the tsar sent builders from Moscow, and possibly Florentine architects arrived with them. In 1726, Metropolitan Sylvester of Kazan and Sviyazhsk consecrated the new temple, as evidenced by an inscription on a wooden cross that was kept in the cathedral's sacristy until 1917.

At the end of 1930, the cathedral's rector, Archpriest Andrei Bogolyubov, was arrested for "anti-Soviet activities" because in 1928 he had sought financial help from the former elder of the cathedral, Pyotr Vasilyevich Unzhenin, who had emigrated to China after the revolution. For the assistance received from Harbin, the 67-year-old priest was sent to the camps.

Starting in 1931, a campaign to close the church began. At a meeting of the political enlightenment committee, comrade Shisranova suggested using the cathedral as a club, reading room, or library, and a resolution was sent to the regional council of the SVB. Soon, the SVB organized anti-religious lectures, agitating for "liberation from religious shackles." All reports were collected for the closure of the church.

During this time, churches were being closed in Kazan, and the Peter and Paul community accepted believers from other churches. Icons and church utensils were brought to the cathedral, including the relics of Saint Varsonofy.

In 1938, mass arrests of priests took place in Kazan, including clergy from the cathedral. Archpriest Mikhail Zosimovsky requested to be removed from registration due to illness.

That same year, it was decided to transfer the building to a museum for an anti-religious museum and lecture hall, but the Foucault pendulum was never installed. In 1939, the cathedral was closed, and Mikhlayev's burial place was looted.

In 1964, a planetarium was opened in the lower church, and in 1967, restoration workshops were placed in the upper church. A conference room was arranged in the altar.

In the late 1980s, the cathedral was returned to the Church thanks to the efforts of the diocese and Kazan intelligentsia. The chief editor of the newspaper "Evening Kazan," Andrei Gavrilov, played an important role. On July 25, 1989, the temple was consecrated by Bishop Anastasius of Kazan and Mari El. The church received the building in a ruined state, but restoration soon began.