In 1928, two monks from St. Tikhon's Monastery in South Canaan, Pennsylvania, hieromonk Panteleimon (Nizhnik) and psalmist Ivan Kolos, seeking greater solitude, purchased a small plot of land near Jordanville in Herkimer County. Soon, another monk from Tikhon's Monastery, Father Jacob, joined them, followed by three more individuals.

By spring 1935, a church in honor of the Life-Giving Trinity was completed. On the Day of Pentecost, the church and the entire monastery were consecrated, led by Bishop Vitaly (Maximenko). On the same day, after the liturgy, a fire broke out on the second floor of the monastery house, and the building burned to the ground within hours.

After World War II, with the arrival of Soviet troops in Czechoslovakia, the Brotherhood of St. Job of Pochaev, which had previously evacuated from Russia after the October Revolution, was once again forced to leave the country. After a brief stay in Munich, the brotherhood accepted an invitation from Bishop Vitaly (Maximenko) to relocate to Jordanville. On December 1, 1946, the Brotherhood, arriving almost in full from Slovakia, joined the monastery's brotherhood. Subsequently, a publishing house was established at the monastery (1946), which began issuing the journal "Orthodox Russia," and the Holy Trinity Spiritual Seminary (1948) was founded. A cemetery was also created for the burial of clergy of the Russian Orthodox Church Outside Russia.

On January 4, 2008, the Holy Trinity Monastery in Jordanville was included in the "list of historic sites in New York State that are at risk of disappearing," compiled by the League for Historic Preservation of the State. The reason was the planned construction of wind turbines near the monastery, which, according to the organization's representative Tanya Verbitsky, could have a "catastrophic impact on the monastery, taking away the tranquility and peace of mind that monks and pilgrims seek here."

On June 23, 2011, the monastery was added to the National Register of Historic Places in the USA.

By the early 2010s, most of the monastery's communications were outdated or severely worn, requiring urgent repairs. In October 2012, the Fund for the Needs of the ROCOR began a charitable campaign to raise funds for the monastery. In December, the First Hierarch of the ROCOR, Metropolitan Hilarion, appealed for help for the monastery.