The wooden church of the Holy Apostles Peter and Paul in Novinki was built in the 1560s and 1570s, although it was originally erected earlier and not in the Novinki settlement, but in the area between the mouth of the Zolotukha River and the building of the Vologda Theological School.

In 1772, a stone church was built on the site of the dilapidated wooden church. This one-story building in the Baroque style resembled the cold church of Vladimir. The bell tower, consisting of a quadrilateral and an octagonal prism, harmoniously completed the architectural ensemble. The church's decor featured innovations: figured pilasters and zigzag moldings above the windows. The church had three chapels: St. Nicholas the Wonderworker, Paul of Obnorsk, and Cornelius of Komel. The chapel of Paul of Obnorsk was likely consecrated in memory of the wooden church of the village of Kobylyno.

Next to the church was a government house for the clergy. The church was visited not only by the residents of Novinki but also by patients of the provincial zemstvo hospital, now City Hospital No. 1. In 1871, a hospital chapel was added to the church in the name of the Icon of the Mother of God "Joy of All Who Sorrow."

On April 6, 1930, the Vologda City Council decided to dismantle churches unsuitable for cultural purposes. A commission consisting of representatives from various departments decided to dismantle the Peter and Paul Church. However, the plans were not realized, but the building lost its completion and bell tower. 11 bells weighing over 115 poods were confiscated and sent for melting down.

In 1937, a butter factory was established in the former church, and in the post-war period, a pasta workshop of Bread Factory No. 1. After a fire in 1990, when the ceilings of the refectory collapsed, the building was not used and gradually fell into disrepair.

By decree of the President of the Russian Federation, the Church of Peter and Paul, dated to the third quarter of the 18th century, was recognized as an object of cultural heritage of federal significance.

In the late 1990s, discussions began about restoring the church near the city hospital. In the early 2000s, the church was assigned to the Church of the Intercession on Kozlen, but the community lacked funds for restoration. Work began in 2008 at the initiative of entrepreneur P.A. Vasev. In October, representatives of various organizations held a cleanup day to clear the area. Before the work began, the rector of the Church of the Intercession on Kozlen, Valery Burkov, conducted a prayer service.

The restoration project, developed by architect Elena Nikitina, was approved by the Department of Culture and the Diocesan Council. In the first three years, the chapel was restored, the bell tower was partially rebuilt, and formwork was made for the vault over the refectory. Work continues on restoring the brick vault and roof. In the coming years, it is planned to resume services in the restored part of the church.