According to church traditions, the first monks settled in this place in the 14th or 15th centuries. The first written mention of the area "Holy Mountains" dates back to 1526 and is found in the notes of the imperial envoy Sigismund Gerberstein.

The first reliable mention of the monastery refers to 1624, when the clergy were granted a royal charter for ownership of this land. In 1679, the monastery was captured and plundered by the Crimean Tatars. The monastery also included the Gorokhovatskaya Mother of God Desert. Later, the monastery was restored and in the 18th century lost its defensive significance, becoming a large landowner.

In 1787, by the decree of Empress Catherine II, the Sviatohirsk Monastery was abolished, and its lands and estates were transferred to the treasury. In 1790, the new owner became Prince Potemkin-Tavrichesky. By the decree of the Holy Synod, the monastery churches were transformed into parish churches, while others were dismantled. The monastery remained in an abolished state for almost 57 years, with the lands remaining in the Potemkin family.

In 1844, at the request of Tatyana Potemkina, by the decree of Emperor Nicholas I, the monastery was restored according to the order and charter of the Glinskaya Desert of the Kursk Diocese. Over the next 70 years, it reached its peak, becoming one of the largest in the Russian Empire. During this period, the assignment of the status of lavra to the monastery was discussed. The monastery had brick workshops, mills, shops, and attracted many pilgrims. At the end of the 19th century, the Spaso-Sviatohirsk skete was established with the Church of Christ the Savior, and the cave Arseniev skete and Akhtyrsk skete were also active. Before World War I, there were about 600 monks in the monastery.

The events of 1917 and the arrival of Soviet power tragically affected the fate of the monastery, which began to be plundered in January 1918. The founder of the Donetsk-Krivoy Rog Soviet Republic, "comrade Artyom," played a role in the fate of the monastery: the main churches were preserved, but a cinema was arranged in the Assumption Cathedral, and a library in the Protection Cathedral.

In 1922, the monastery was liquidated, and a House of Rest for the workers of Donbass was established in its place, leading to the final ruin of the monastery.

The Sviatohirsk Monastery was reopened in 1992. The first inhabitants were monk, priest Seraphim and four young novices from Donetsk. That year, the plundered and desecrated Assumption Cathedral, which had been turned into a cinema, was returned to the monastery. In 1995, with the increase in the number of brethren, the restoration of the churches and buildings began.

On November 28, 2003, the buildings that were under the management of the Slovyansk Historical and Architectural Reserve and the "Holy Mountains" sanatorium were transferred to the monastery. Considering the antiquity of the monastery and its historical role, on March 9, 2004, the Holy Synod of the Ukrainian Orthodox Church granted the monastery the status of lavra, making it the third Orthodox lavra in Ukraine after the Kyiv-Pechersk and Pochaiv Lavras.

On December 5, 2005, the episcopal ordination of the abbot of the lavra, Archimandrite Arseniy Yakovenko, took place. On July 12, 2008, the Assembly of Holy Fathers who shone in the Holy Mountains on the Donets was glorified. The assembly included 17 saints. The decision to canonize 16 of them was made on May 8, 2008. Blessed John, the hermit of Sviatohirsk, was glorified in 1995.

On July 7, 2009, the brethren of the monastery discovered the relics of Archimandrite Arseniy Mitrofanov and Blessed Isaac Golovin. The Assumption Sviatohirsk Lavra is a significant spiritual center for the Orthodox flock of eastern Ukraine. The Assumption Cathedral, the monastery bell tower with the Protection Church, and the oldest church in honor of the Blessed Anthony and Theodosius of the Caves have been restored. The churches in honor of Blessed Alexius and Saint Nicholas have been restored. The All Saints skete with a wooden church has been revived.

All churches, caves, and surviving buildings have been returned to the monastery. More than a hundred brethren serve in the monastery. In the summer of 2014, the monastery sheltered 800 refugees, including 300 children. The Holy Synod of the Ukrainian Orthodox Church designated the lavra as the residence of bishops Innocent Shestopal and Hippolytus Hilko.

The first monks dug out the churches and cells in the upper tier. Light penetrated through small window openings, illuminating the transom for the icon and other elements. The cells connect to a square hall supported by a massive pillar. The eastern wall shows traces of the iconostasis of the first underground church up to 1632. It was initially called the Assumption Church, then the Nicholas Church, and in the 19th century, the Church of John the Baptist.

From this church, the labyrinths of sidewalks and cells branch out. One sidewalk connects it to the refectory, another leads to the lower tier with the Alexiev cave church. In 1753, the schismatic Chekmenyev was exiled here. The altar part of the church had the shape of a segmental transom and was separated by pilasters.

Inside the chalk mountain is the church of the Blessed hermits Anthony and Theodosius. A corridor carved into the chalk leads to the main place in the church. It was founded by followers of the Kyiv monks who fled from the hordes of Batu. Archaeologists found pottery from the 8th and 10th centuries here.

On the chalk cliff are the remains of a three-chamber Nicholas church in the Sloboda Baroque style. In 1679, three chalk cones with windows stood on this site. The cave Assumption church partially collapsed, exposing the interior. The church complemented the lost part of the rock and became its decoration. Its domes are oriented along the east-west axis. Ukrainian masters of the 15th and 16th centuries often placed an octagon of larger volume on top of an octagon of smaller volume. Above the altar rises a pyramidal tower with a dome. The western tower is adorned with decorative brick ornamentation.