The church was deconsecrated in the reforms of Emperor Joseph II and in 1785, with the neighboring house for retired priests, it was converted into a military depot and barracks.
In 1921, the Czechoslovak Orthodox Church was founded, and gained then unused temple, which they reconstructed and it became the main Orthodox Church of Czech lands and a cathedral, seat of bishop.
Today, the Cathedral of Ss Cyril and Methodius is most known due to Operation Anthropoid.
After the successful assassination on Reichsprotektor Reinhardt Heydrich on 27tn May 1942, the group of seven brave Czechoslovak paratroopers were offered a shelter in Church´s krypt. Unfortunately, after few days, the SS troops discovered them and attacked the church. The paratroopers resisted and in last minute, before the SS would capture them, they committed suicide. Their last words were: "We will not surrender. Never. We are Czech."
The Operation Anthropoid resulted in furious vengeance of the Nazis. The towns Lidice and Ležáky were exterminated, all men killed, women and children abducted in the concentration camps. Bishop Gorazd and other representatives of the Czech Orthodox Church and their family members were executed for sheltering paratroopers. Nowadays, in the Church and in the crypt is the National Monument to the Heroes of the Terror of Heydrich.