The history of the Trinity Monastery in Astrakhan begins in 1568, when Tsar Ivan the Terrible sent Abbot Kirill with the task of founding a monastery of St. Nicholas the Wonderworker in the city. By 1573, Abbot Kirill had erected the Church of the Life-Giving Trinity with a refectory, a cellar, 12 cells, two cellars, a garden, and a kitchen. All buildings were wooden and surrounded by a wooden fence. By the time of Abbot Kirill's death in 1576, two more wooden churches had appeared in the monastery: the Church of the Entry into the Temple of the Most Holy Theotokos and St. Nicholas the Wonderworker. Initially, the monastery was called the Nicholas Monastery, but later it was named the Trinity Monastery in honor of the cathedral church of the Life-Giving Trinity, consecrated on July 25, 1576. In the 1590s, the new abbot Theodosius began the reconstruction of the monastery from wood to stone. By September 13, 1603, the new stone Trinity Cathedral was consecrated, to which a chapel in honor of the Holy Passion-Bearers Princes Boris and Gleb was later added. Under Abbot Theodosius, a stone bell tower with the Church of St. Nicholas the Wonderworker and a wooden church of the Origin of the Honorable Wood of the Cross of the Lord were also built. In 1606, under the new abbot Ion, the construction of the stone Church of the Entry was started, with refectory chambers adjoining the Trinity Cathedral. However, the completion of the construction was delayed due to the Time of Troubles, and the church was consecrated only in 1620. In 1619, under Abbot Raphael, the construction of the stone Holy Gates with the Church of the Entry of the Lord into Jerusalem began, completed a year later.

After the 1917 revolution, the Trinity Cathedral underwent many trials. In January 1918, during the battles in Astrakhan, the church was closed by the decision of the revolutionary authorities. After the consistory was destroyed, its refectory was used to house an archive, which ended up in disarray. The Trinity Church and part of the Kremlin were fenced off, making it difficult for believers to access. Services were held rarely due to the small number of the congregation. In October 1928, the Soviet authorities finally seized the church, looted it, and the iconostasis was destroyed and burned. In the 1950s, the archive was moved, and in the 1970s, restoration work began. Nothing has survived from the ancient relics of the monastery, but the monastery itself remains an important spiritual value. The first Astrakhan archbishops: Onuphrius, Macarius, and Raphael are buried here. The monastery brotherhood was buried around the cathedral, and to the north of the church, according to legend, lies a mass grave of 441 Astrakhan residents killed by the order of Stepan Razin. The Trinity Monastery also preserves the memory of the holy martyr Joseph, who rose from novice to archimandrite.