The monastery was founded in 1533 by St. Trifon of Pechenga at the confluence of the Mana River, now known as Nama-Yoki, with the Pechenga River. In 1548, after Trifon left the monastery, the brethren independently moved it closer to the mouth of the Pechenga, to a more convenient location for fishing and trade.

In December 1589, the monastery was attacked by a Finnish detachment, subjects of the Swedish king. All those in the monastery were killed, and the monastery was burned down. After this, the monastery was relocated to the territory of the Kola fortress, near the Church of the Annunciation of the Holy Virgin.

After a fire in 1619, the monastery was again moved to a new location, across the Kola River, where a cathedral church was built in honor of the holy apostles Peter and Paul. However, in 1765, by order of Empress Catherine II, the monastery was abolished.

Only in 1886, by decree of the Holy Synod, was the monastery revived at the mouth of the Pechenga, at the site of the martyr's death.

After the October Revolution, at the end of 1920, the monastery was plundered. During the Soviet-Finnish War, the monastic community evacuated to Finland and became part of the New Valamo Brotherhood, while the abbot, Hieromonk Paisiy Ryabov, was arrested by Soviet security services and executed on December 12, 1940. The last of the Pechenga monks, Father Akakiy, died on January 30, 1984, at the age of 110.

In 1997, the Russian Orthodox Church announced the revival of the monastery. It houses the relics of 116 martyrs who perished during the devastation in 1589. Since 2008, a monastery dependency has been operating in Murmansk.

In November 2007, the authorities of the Pechenga District of the Murmansk Region decided to transfer historical lands to the monastery in the area of the village of Luostari, where the grave of St. Trifon of Pechenga was located, as well as the graves of martyrs Jonah and German.

On December 1, 2007, a fire occurred at the monastery, completely destroying the Main Church. It was decided to restore the monastery to its original appearance of the early 20th century in the village of Luostari, Pechenga District, Murmansk Region.

By December 2012, the church in honor of the Life-Giving Trinity was consecrated, and by that time, almost all buildings had been rebuilt.

Currently, about 10 people live in the monastery, including 3 monks.