A partial impression of the original planned appearance of the church is provided by the Chapel of St Barbara, which was built first so that mass could be celebrated.

Count Wenceslaus Kolowrat-Liebsteinsky (1634 – 6 October 1659) from the prominent Czech House of Kolowrat was the largest patron of the Church of St. Nicholas.

The massive nave with side chapels and an undulating vault based on a system of intersecting ellipsoids was apparently built by Christoph Dientzenhofer.

[3] The pillars between the wide spans of the arcade supporting the triforium were meant to maximize the dynamic effect of the church.

The chancel and its characteristic copper cupola were built in 1737–1752, this time using plans by Christoph's son, Kilian Ignaz Dientzenhofer.

Following the abolition of the Jesuit Order by Pope Clement XIV, St Nicholas became the main parish church of the Lesser Town in 1775.