The original building dates back to approximately 1100 and was consecrated to St Nicholas patron saint of all merchants and was related to the pre-urban settlement called Ujezdec situated in front of Znojmo Castle gates.
In 1190 the newly founded Louka Abbey to the south of Znojmo was gifted with the church by Conrad II Otto, the Duke of Bohemia.
In the 13th century the church became incorporated into the City of Znojmo.
In 1335 during the Great Fire of Znojmo the old church was burnt to the ground. In the following decades a completely new church structure was erected – this is the present Gothic church.
It was re-built several times in the 15th century.In December 1437 the dead body of Holy Roman Emperor Sigismund was publically displayed inside the church.
During the Baroque period the church altars, statues, paintings and side chapels were modified.The present church tower was built as late as in the mid-19thcentury.