The appearance of this church is linked to an important event in the history of Astrakhan. In 1670, the city was captured by Cossacks led by Stepan Razin. They ruled Astrakhan for almost two years, responsible for the execution of many citizens, and on May 11, 1671, they killed the Astrakhan Metropolitan Joseph after brutal torture. In November 1671, royal troops commanded by Voivode Ivan Bogdanovich Miloslavsky approached the city. After lengthy negotiations, the weary citizens of Astrakhan agreed to surrender the city peacefully on November 27, the day of the celebration of the Icon of the Mother of God 'Sign'. In honor of this event, at the initiative of Voivode Miloslavsky, a wooden Sign church was built. It is difficult to name the exact date of construction, but it is likely that the church began to be erected immediately after these events. By 1672, it might have already been completed and consecrated by the new Metropolitan Parthenius.

The church was located in the southern part of the White City, right by the walls. Nearby was a cemetery and possibly a women's monastery. However, the assumption that there was a monastery associated with the Sign church is incorrect, as the Annunciation Women's Monastery already existed in Astrakhan in 1671. The monastery was simply located next to the Sign church, which was a parish church.

After October 1917, the Sign church went through difficult times. In January 1916, during battles, the church was under threat. There was a rumor that white Cossacks were shooting from the church bell tower with a machine gun. The Bolsheviks took this seriously and decided to blow up the church, but by God's mercy, this did not happen. The church miraculously survived the fire that destroyed the center of Astrakhan. Everything around the church burned down, except for the Sharlau confectionery, and it remained a miraculous island amidst the flames. Unfortunately, all the buildings in the churchyard burned down.

Soon, a significant event for the Astrakhan church and city took place in the Sign church. On May 24, 1919, the glorification of the Holy Martyr Joseph, Metropolitan of Astrakhan, took place. This event had long been awaited by the people of Astrakhan, but in December 1918, access for believers to the Kremlin, where the relics of the saint were located, was restricted. The headquarters of the 11th Red Army was located in the Kremlin, and military authorities gradually occupied church buildings. On May 23, the day before the glorification, the authorities banned services in the Assumption Cathedral and sealed it. This was an attempt to hinder the celebrations, but Archbishop Mitrophan Krasnopolsky blessed the service to be held in the Sign church. This was symbolic, as the foundation of the Sign church is associated with the name of Holy Martyr Joseph, who was killed by the Razinites, and through whose prayers Astrakhan was liberated. On the day of glorification, May 24, an attempt was made to conduct a procession from the Sign church to the Assumption Cathedral, but military authorities did not allow the believers to pass.

After the seizure of the Nativity of the Mother of God church by Renovationists in the spring of 1924, Archbishop Faddey Uspensky moved the episcopal see to the Sign church, which became a cathedral. However, a week later, it was also seized by Renovationists. They remained in the church until 1930, when it was taken from them and handed over to the central club of pioneers. But the club never settled in, and on July 2, 1930, a construction training point was opened in the church premises. Unlike many Astrakhan churches, the Sign church retained the main part, losing only the upper part with the domes and bell tower, and was repurposed into a bakery. In this form, the church exists to this day.