Originally built in the 13th century, it was partially destroyed in the Soviet bombing of Tallinn in World War II.

[3] While the city was still unfortified, the church had heavy bars for closing the entrances, loopholes and hiding places for refugees.

The resulting fire turned the church into ruins and destroyed most of its interior (except that of St. Anthony's Chapel), including baroque pews, lofts and pulpit.

[2][6] Most famous of the artworks in the museum is perhaps a Danse Macabre by the Lübeck master Bernt Notke, which depicts the transience of life, the skeletal figures of Death taking along the mighty as well as the feeble ones.

Only the initial fragment of the original 30 metres (98.4 ft) wide painting (accomplished at the end of the 15th century) has been preserved and is currently displayed in St Nicholas Church.

The former High Altar of St Nicholas Church was made between 1478–1481 in the workshop of Hermen Rode, a master painter from Lübeck.

[2][5] A single panel painting by the Master of Schloss Lichtenstein, "Presentation of Christ in the Temple" (1430–1440) and several medieval woodcarvings by Henning von der Heide (depicting St. Nicholas, Virgin Mary and John the Evangelist) (1510–1520)[10] are also on display.

[11] Of later works of art, the figure of St. Christopher by Tobias Heinze, (1624)[10] a 350-year-old decorative screen of Bogislaus Rosen's chapel carved by Frans Hoppenstätt,[2] and the epitaph of Antonius von der Busch by Arent Passer (1608)[10] can be mentioned.

Around the nave lie a series of 17th century tomb-top effigies like Berndt Reinhold von Delwig and Hermann Nieroth in full body armour.

The air conditions in the chapel where the body was held protected the corpse from decaying and it became an attraction, remaining on display until 1897, when the authorities finally buried it.