The idea of creating a church in the settlement of bridge builders emerged in the second year of construction of the railway bridge over the Ob River. The decision to build it was made on October 10, 1895, at a meeting of the settlement's residents. They decided to appeal to the Tomsk bishop Macarius with a request to close the "taverns and dens" and instead build a church in the name of Saint Alexander Nevsky. The church was conceived as a monument to Emperor Alexander III, the inspirer of the construction of the Great Siberian Railway, "which he had conceived and founded." They decided to build it near the railway bridge, at the boundary where the Middle Siberian section of the railway began.

At a general meeting of the population, it was decided to rename the settlement Krivoshchekovsky to Alexandrovsky in honor of the church being built in the name of the Holy Blessed Prince Alexander Nevsky. However, this name was not recorded in any documents, only mentioned in the "Tomsk Reference Sheet." Later, many years later, the Novonikolaevsk City Duma planned to erect a monument to Alexander II in Novonikolaevsk for the 50th anniversary of the liberation of the peasants from serfdom, opposite the Alexander Nevsky Cathedral, at the junction formed by Kabinet Street and Nikolayevsky Avenue. A commission was organized to raise funds for the construction of the church, led by the chief engineer of the railway section, Nikolai Mezheninov. It included engineers Berezin, Korolev, Livenkov, Link, peasant Vagin, merchant Zhernakov, forester Imshenetsky, merchant Mozharov, and others.

The construction of the church required significant expenses. The majority of the funds were allocated by the ruling house from the fund named after Emperor Alexander III, established by Emperor Nicholas II. The money from this fund was directed towards the construction of churches in areas of resettlement along the Siberian Railway. By 1904, 214 churches had been built at a total cost of about two million rubles. Nicholas II himself donated five thousand rubles from the funds of His Majesty's Cabinet and allocated 2,400 square fathoms of land for the church free of charge. Later, he added another six and a half thousand rubles for the construction of the church. Voluntary contributions were made by railway workers, laborers, road builders, and merchants.

Understanding that the construction of a church for 500 people would take several years, they decided to open a temporary wooden prayer house. It was built in a month with charitable funds, and the altar was consecrated in honor of Saint Alexander Nevsky. With the opening of the church, the prayer house was abolished. Its location is unknown; it is assumed that a church in honor of the Protection of the Holy Virgin was built in its place. In November 1898, before the construction of the Alexander Nevsky Church was completed, a new wooden church in the name of the Prophet Daniel was consecrated in the Novonikolaevsk settlement near the Ob railway station, becoming the oldest church in the Novonikolaevsk settlement.

Engineer Nikolai Tikhomirov, who had previously led the construction of the last span of the bridge, was appointed to oversee the construction of the Alexander Nevsky Cathedral. On March 31, 1897, "proper" traffic was opened across the bridge, and Tikhomirov was transferred to another work site. He was a responsible and fair man, so he was entrusted with this unusual task. His wife Maria Ananyevna recalled: "At every responsible moment, he took me with him, ran around the entire building, saying: 'You will live long, look, there will not be a single crack, but in St. Petersburg, Isaac is always under scaffolding.'

On May 15, 1897, the laying of the church took place. The service was attended by the Tomsk governor, the head of the Altai mining district, engineer Mezheninov, the chief construction engineer Tikhomirov himself, and a large number of residents of the settlement. Construction began actively. The ribbon foundation of the church was made of natural rubble stone. Initially, the walls were planned to be laid in rows of light and dark bricks, but this idea turned out to be too costly, and they abandoned it, opting for red brick instead. The complex masonry was carried out by Italian stone masons. The floors were laid on metal plates, and the floor tiles were specially brought from Holland. The outer walls were whitewashed, and the interior painting of the church was done by icon painters from the first Siberian workshop of Joseph Pankryshev in Tomsk.

By the end of 1898, the wall masonry was completed, and on December 29, 1899, the Tomsk and Barnaul bishop Macarius consecrated the main altar of the Alexander Nevsky Cathedral. In 1904, the side chapels of the church were consecrated in the name of Saint Nicholas the Wonderworker and in the name of Saint George the Great Martyr and Victorious. The church became not only the most beautiful building in the settlement but also the largest church structure along the entire Great Siberian Railway.

A year later, the construction manager Nikolai Tikhomirov unexpectedly died from a brain hemorrhage. For his merits, he was buried within the church's enclosure. A granite slab with the inscription in golden letters was placed on his grave: "Here lies the remains of the builder of this church, Tikhomirov Nikolai Mikhailovich."

In 1971, workers discovered a crypt with Tikhomirov's body during construction work. On August 18, 1971, the executive committee of the Novosibirsk City Council decided to rebury the remains at the Zaeltsovsky cemetery. They were reburied and forgotten. No street or alley was named after Tikhomirov, only a stop near the Chulymskaya station.

During the Soviet era, the church had to endure difficult times, although it was not destroyed. In 1938, by the decision of the Novosibirsk City Council, the cathedral was closed, the bells and crosses were removed, and the bell tower was destroyed. During the Great Patriotic War, it housed the design institute "Promstroyproekt." The building was partially reconstructed: window frames were replaced, a ceiling was built in, and the facade masonry was partially disrupted. The painting was completely destroyed. In 1957-1958, the former church housed the West Siberian studio of newsreels, which again redesigned and spoiled the architectural monument. Only in September 1989, by the decision of the regional executive committee, the building was returned to the Novosibirsk Diocesan Administration of the Russian Orthodox Church.

In 1991, the Alexander Nevsky Cathedral was consecrated again by His Holiness Patriarch Alexy II. After restoration work, it once again became one of the most beautiful buildings, delighting believers, residents, and guests of Novosibirsk.