The monastery is supposed to date back to unremembered times. The first monks lived in dug-outs in the hillock. A vaulted tomb (bone-vault), used for praying during fasting periods by the monks, has been excavated.
In 1872 one of the biggest destructions of the monastery happened. In this year the Turkish treasury was robbed at the Arabakonak pass and soon after that the Apostle of freedom, Vassil Levski, was captured. At that time, lots of the monasteries were set on fire including the Chepintsi cloister. It was entirely built of wood and only the stone foundations were left. At the time of destruction, twenty-four monks lived in the monastery, some of them were sent in exile to Diarbekir (Asian Turkey).
Nayden Kentrov, one of the monks, who survived after the exile, was the initiator of building a fountain in the space of the monastery and putting the following inscription on it: “God bless him who drinks water from this fountain, and god forgive him when he dies”.
An old lady living in Chepintsi, known as grandmother Gesha, had a dream with three angels which would not leave her until a monastery is built. So, in 1906 a new monastery was started in the place of the old one. It was dedicated to St. Three Saints, as according to the old lady’s words.
The official holiday of St Three Saints is celebrated on January 30. But there are some several religious holidays (Ilinden, St Holy Spirit and the Birth of God’s Mother), when lots of people gather at the monastery. Apart from the main church, the present-day monastery also has two new chapels dedicated to St Petka and St Prophet Ilia. In 1993 a new residential building for the nuns was built. Another small church, Shatovska church, built in 1906, is also a part of the complex.