In the late 16th century, a stone fortress known as the Kremlin was built in Putivl on the site of an ancient Russian wooden fort. It had a hexagonal shape with round corner towers and a square gate tower. The fortress walls were relatively low and had three tiers of embrasures. The French traveler Jacques Margeret, who visited Putivl, noted that in Russia, castles and fortresses were mostly wooden, except for Moscow, Smolensk, Ivan-Gorod, Tula, Kazan, Astrakhan, and Putivl.

In 1592, knowing the reliability of the Putivl fortress, monks from the suburban Molchenskaya Pustyn settled here. They built a stone church dedicated to the Nativity of the Blessed Virgin Mary and soon transformed the fortress into a monastery. The monks were obliged to defend the monastery-fortress in case of an attack.

The history of the Molchensky Monastery is closely linked to the "Time of Troubles." In 1598, after the death of Tsar Fyodor Ivanovich, the Rurik dynasty ended, and Boris Godunov ascended the throne. Rumors circulated that Tsarevich Dmitry had been killed on Godunov's orders. Monk Grigory Otrepyev, fleeing to Poland, began to pose as the surviving Tsarevich Dmitry. Polish nobles decided to use the "False Dmitry" for their purposes and sent an army to Moscow, hoping to seize Russian and Ukrainian lands. The usurper promised the lands of Putivl to his patron, the Sandomierz voivode Yuri Mnishek.

In the battle near Dobrynichi, Godunov's army defeated False Dmitry, who retreated to Putivl, where he fortified himself. Putivl and other cities of the Severian land sided with him. Historian N.M. Karamzin explains this by saying that the "old Lithuanian spirit still lived here," while Dutch merchant Isaac Massa called Putivl the "head and instigator of all rebellious cities."

False Dmitry made the stone fortress, specifically the Cathedral of the Nativity of the Blessed Virgin Mary of the Molchensky Monastery, his residence in Putivl. His room was located in the upper tier of the main tower of the cathedral. For four months, he sent letters announcing his "miraculous salvation" and calling for a fight against Godunov.

Gathering a new army, the usurper moved towards Moscow in 1605. At that time, Boris Godunov died, and False Dmitry managed to seize the throne. However, a year later, he was killed.

During the "Time of Troubles," the Molchensky Monastery was repeatedly burned and was consecrated anew in 1630. At the turn of the 17th-18th centuries, it was reconstructed in the style of Ukrainian Baroque. By the end of the 17th century, having lost its significance as a fortress, Putivl fell into decline. The fortified town became a provincial district town.

The Molchensky Monastery also fell into decline. Under Catherine II, it lost its lands and was downgraded to a "3rd class monastery." In 1917, the "October Revolution" destroyed the old foundations.

In the early 1920s, the monastery was ravaged and looted, and after a fire, it was abolished. In the 1940s, it was converted into a vocational school, and in the 1950s, a radio parts factory was located there. However, the crosses on the cathedral remained.

In 1987, the monastery became part of the Putivl Historical and Cultural Reserve. In 1992, it was returned to the church and became a male monastery again. Since 1997, by the decision of the Synod of the Ukrainian Orthodox Church, the monastery became female. Restoration of the ancient monastery, a unique architectural monument of the 17th century, began thanks to the efforts of believers and nuns.