The church was named in memory of the Transfiguration of Jesus, which allegedly took place on Mount Tabor (Hebrew: הר תבור) in today's Israel.

The oldest surviving section of the church is its 13th-century choir, built from granite ashlars in late Romanesque style with a rib vault.

In 1352 – as preserved in a document – Heinrich Billerbeck, the "rector ecclesie in alta schonehusen" (parson of the church in Hohenschönhausen), unmasked a man pretending to be the late Waldemar 'the Great' of the Margraviate of Brandenburg, declared dead in 1320.

The present prayer hall of two naves is an addition of about 1450 erected from simple boulders and with a vaulted roof supported by a central square pier.

In 1626 – in the course of the Thirty Years' War (1618–1648) – the Lutheran Swedish troops under Gustavus II Adolphus and the Catholic Imperial Army under Wallenstein ravaged Hohenschönhausen and plundered the church.

Their leaves were to be picked by village schoolchildren and delivered for use in the loss-making silk production the king tried to enforce in his dirigist concept of cameralism.

[3] In 1952 the congregation had to demolish the dilapidated domed top of the tower because in the communist planning system – even seven years after the war – there was a shortage of construction material, at least if needed for a church building.

The original altar, depicting Mary(am) of Nazareth, was translated in 1924 to St. Nicholas' Church in Berlin's central borough of Mitte and is now exhibited in the Märkisches Museum.