The construction was begun probably in place of the Saint James Chapel. The financing of the church was partly done by the citizens, partly from the income of indulgences. (The first related document from 1349, signed by the archbishop of Avignon and fifteen other bishops grants the indulgence for those contributing to the illumination and furniture of the Saint Michael Church). The construction was completed between 1442-1447, the old tower was built between 1511-1545. The tower that stands today was erected in 1862. The oldest of its sections is the altar, inaugurated in 1390, while the newest part is the clock tower, which was built in Gothic Revival style (1837-1862).
The church was Protestant between 1545-1566, and Unitarian in the period 1566-1716, after that it was re-confiscated by the Catholic Church during the counter-reformation.
Some important historical events that took place in the church:
- 26 July 1551: Queen Isabella of Hungary gives the Hungarian Crown to General Castaldo, the deputy of Ferdinand I, and cedes with that Hungary and Transylvania
- 23 October 1556: Queen Isabella returns and takes back the reign of Transylvania, in the name of her son, the child John II Sigismund Zápolya
- 27 March 1601: the third investiture of Sigismund Báthory as Prince of Transylvania
- 12 February 1607: election of Sigismund Rákóczi as Prince of Transylvania
- 7 March 1608: election of Gabriel Báthory as Prince of Transylvania
- 13 October 1613: election of Gabriel Bethlen as Prince of Transylvania
- 18 May 1944: the speech of Áron Márton, bishop of the Roman Catholic Church in Transylvania in which he condemned the deportation of Jews.