The brick church, dating from the 13th century, was a well-known pilgrimage site for the black cross in the chapel on the northern side of the church (the cross is now depicted on Pärnu's coat of arms). The church had collapsed and was rebuilt from 1590-1600, when it was consecrated. It was last renovated in 1886-1887. Though primarily German Lutheran, the church was Roman Catholic during Polish rule from 1582-1617. The Nicolai parish merged with the Elisabet parish in 1940, which was named Pärnu Niguliste parish. The church sustained damage from several fires and wars. It burned down in 1944, leaving only the outer walls. The church remains were blown up during Soviet times in 1953. In 1989, a memorial to the church was established on the site by former residents who had resettled in Germany.
