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In the late 1980s missionaries serving in the Finland Helsinki Mission began to contact Soviet citizens who were visiting Finland. Also, Finnish Latter-day Saints started traveling to Estonia, then part of the Soviet Union, where they began to spread the gospel. Tallinn, Estonia’s capital, was one of these initial contact points.

The first branch (a small congregation) organized in the former Soviet Union was in Tallinn on January 28, 1990, presided over by a Finnish missionary, Hari Aho. Peep Kivit later became the first native branch president. In September 1991, two more branches in Tallinn were organized, one Estonian speaking, the other Russian speaking. The two Estonian branches were combined in the summer of 1997.

The Church received government recognition in Estonia on 2 July 1990. However, new Estonian laws passed in 1993 required that the Church be re-registered. In 1994, through the efforts of Jussi Kemppainen and senior missionary James Ames, the Church fulfilled its registration requirements. The first chapel in the Baltic nations was dedicated in Tallinn in November 1999. The Book of Mormon in Estonian was published in January 2000.