Originally established by Charles IV in 1347 as Na Slovanech, the Emmaus Monastery of Prague was once the only Benedictine abbey not only in Bohemia but in all of Slavic Europe, serving as its center of learning and art. The name comes from a town mentioned in the Gospel of Luke of the New Testament.

Over the centuries, the church underwent a number of renovations, incorporating a variety of architectural styles from Gothic to Baroque, even showing Pagan influences in some elements.

Legend has it that, once upon a time, the devil came up to the monastery to corrupt the famously pious monks of Emmaus, taking the form of the recently deceased cook. Cooking delicious delicacies, the devil managed to turn the monks into fat sluggards, until the abbot discovered his diabolical intentions and banished him. It is said that the monks went on to be doubly pious afterward.

During World War II, the monastery was seized by the Gestapo and the monks were sent to the Dachau concentration camp. Furthermore, a U.S. bombing raid on Prague destroyed much of the building on 14 February 1945, which left it in a desolate state until the 1960s, when the current, somewhat futuristic roof was built on top of the medieval church.