Since the Parish Church of St John was too small to accommodate the large congregation, it was decided that a new church be built to serve the Estonian speaking members of the parish, while St John's would be used by the German speaking members.

In 1889 a new altar painting was commissioned for the church by Julie Emilie Wilhelmine Hagen-Schwarz, a well-known Baltic German artist based in Tartu.

Above the picture was an inscription from scripture which said Nida om Jumal ma ilma armastanu (For God so loved the world) (John 3:16).

Several hundred buildings were destroyed in the fire, including St Mary's Church.

After World War II, the occupying Soviets denied the congregation access to the church or permission to restore the building.

In 1956, the Tartu city authorities gave the ruins of the church building to the Estonian Agricultural Academy and a gym was built instead, designed by I. Kalmet.

The congregation provided essential equipment and converted the former gym into a temporary church space.