According to legend, during the Crimean campaign of 1770, the headquarters tent of A. V. Suvorov was located on the northern border of the Old Town. Later, a wooden church was built in honor of Saints Constantine and Helena at this site. At that time, the population of Simferopol was about 1,000 people, not counting the military. The church was small and soon could not accommodate all the parishioners. In 1801, the Holy Synod granted permission to build a new church, but work only began in 1805 when the parish gathered the necessary funds. The new wooden church was more spacious and took about a year to build. In the autumn of 1806, it was consecrated in honor of the apostles Peter and Paul. It was a small rectangular building with a bell tower cast from the remnants of the Ak-Mosque mint. The wooden church was famous for its beautiful iconostasis, but it had no frescoes.

Twenty years later, the church became dilapidated and was dismantled. Soon, the Alexander Nevsky Cathedral was built in the city, where the bells and church utensils were transferred. However, the residents wanted to revive the Peter and Paul church, and from 1866 to 1870, the construction of a new building began. The project was developed by architect Konstantin Lazarev. The residents collected 32,000 rubles, and the Synod allocated another 23,000. Construction progressed quickly, but finishing work continued until 1870. The church was built in the style of classicism with elements of ancient Russian architecture and had a magnificent iconostasis. The building was erected in the shape of a cross with a high bell tower. In 1870, the cathedral was consecrated in honor of the apostles Peter and Paul. In 1868, a church parish charity and schools opened at the cathedral. In 1890, the churchyard was enclosed with a metal fence and planted with trees. In 1902-1903, artists painted the dome and walls, turning the church into a gem.

In 1937, the authorities banned services in the cathedral, and the building was used as a warehouse. Over time, it fell into disrepair. In the late 1980s, restoration of the cathedral began. Architect Olga Sergeeva and S. L. Belova found documents that allowed them to recreate the dome and bell tower. In the 1990s, climbers and restorers worked on the restoration. On July 12, 1991, a service was held in the church again. In 2003, the cathedral became the cathedral of the Simferopol and Crimean diocese. In 2004, an imprint of an icon appeared on the glass of the icon case, which was set up for veneration. The cathedral houses relics, including an icon of the Holy Trinity with a piece of the Lord's robe. In 2008, a service was held in honor of Archbishop Guriy Karpov. In 2016, his relics were transferred to the Alexander Nevsky Cathedral.