The church dedicated to Saints Flora and Lavra is mentioned as early as the beginning of the 17th century. Initially, it was wooden and had an altar in honor of Saints Cosmas and Damian. The church was located in a settlement named after it, Florovskaya, one of the oldest in Tula, situated beyond the Nikolsky Gates of the Earthen City. These gates were approximately where Metallists Street intersects with Soviet Street today. By 1710, the church was already made of stone, and in 1748, with funds from parishioners, a stone altar of Cosmas and Damian was built. Around the same time, an altar in honor of the icon of the Mother of God "Sign" appeared. By the early 1770s, the church had fallen into disrepair, and it was decided to build a new building in honor of the Bogolyubskaya Most Holy Theotokos with altars of Flora and Lavra on the right and Cosmas and Damian on the left. The altars were first built and consecrated in 1779, while the main altar with the iconostasis was completed by 1796. From that time, the church was officially called Bogolyubskaya, but the name Flora and Lavra remained in popular use.

The architecture of the church combines elements of Baroque and Classicism. The refectory was built with Baroque elements, such as rounded corners and a mansard roof, while the church building itself features strict columned porticos and a smooth drum, characteristic of Classicism. However, Baroque details have also been preserved in the architecture, such as the faceted dome and decorative lucarnes. The interior space of the church is unique in that it has no supporting columns, with all the load transferred to the vaults. The architect of the main volume of the temple is considered to be K.S. Sokolnikov, although some researchers believe he participated in the construction of the bell tower. Until the 19th century, the old bell tower remained with the church, but in 1806, a petition was submitted for the construction of a new one, completed by 1830. In 1834, the largest bell weighing 519 poods was acquired, funded by merchant Poddelshchikov.

The main shrine of the temple was the Bogolyubskaya icon of the Mother of God, known for its miracles, especially during epidemics. In 1892 and 1893, fearing cholera, the people of Tula replaced the silver vestment of the icon with a golden one adorned with diamonds, made in 1894. The church also housed an ancient walnut cabinet for storing books and utensils, traditionally believed to have been brought from Holland by merchants Luginins. Saints Flora and Lavra were considered patrons of horse breeding, so on their feast day, people gathered at the church to bless horses. In 1894, a church parish school was opened at the church.

In the 1925 directory, the church of Flora and Lavra was classified as belonging to St. Petersburg Baroque. In 1929, a decision was made to demolish the church, but it was saved due to its recognition as a monument of 18th-century architecture. In the 1930s, the temple was closed and transferred to a weapons factory, where a dining room and warehouses were located. By the early 1970s, the building was in disrepair, but in the mid-1970s, conservation work was carried out. In 1991, the church was placed under state protection as a monument of history and culture.

In 1990, the church was returned to the Tula Diocese. It was in a deplorable state: without heating and lighting, with broken windows and a cemented floor. It was necessary to manually break the concrete and remove it. By December 1991, heating, roofing, and finishing works were carried out, and a new porch was built. Today, a library and Sunday school operate at the church.