The Church of St. Nicholas is is mentioned in sources as early as 1273. It was originally a parish church and had a long tradition as a centre of preaching, with Milíč of Kroměříž, Matěj of Janov and other representatives of Hussitism and the Reformation all preaching here. In 1497 had the church 2 towers, the cemetery was nearby, the charnel-house and school also.

Ferdinand III decided to invite Spanish Benedictines monks into Prague. In 1635 the church came into the possesion of Benedictines from Emazy monastery, who started to build a monastery there. The construction of the monastery lasted from 1727 to 1730, and when it was completed work was started on a new church which was finally completed in 1735. The plans were designed by the famous prague baroque architect Kilián Ignác Diezenhofer. The structure is one of his masterpieces and it attracts by the sofistically divided inner space and interesting light scheme. The new church building was consecrated in 1737.

Both the church and the monastery were closed down in 1787 as part of reformes of Josehp II, and the valuable interior fixtures were sold off and removed. The church itself was taken over by the Prague municipal authorities, who in so doing de facto protected in from dilapidation. In 1865 the church was used temporarily for cultural purposes, after having been adapted for use as a concert hall. In 1871 it was once again used fot the celebration of divines services, when it was rented by the Russian Orthodox Church. The monastery was demolished in 1898. On the site where it had stood a neo-baroque residential building was contructed in 1902.