In 1989–1993, with the fall of communism, the city of Prague endeavored to restore Sts. Simon and Jude, including the installation of floor heating to facilitate comfortable use year-round. The church was never reconsecrated, and the maintenance of Sts. Simon and Jude was handed over to Prague Symphony Orchestra in exchange for its use as a concert hall. In 2000 the historic pipe organ was overhauled by organ builders Jaroslav Tůma and Vladimir Slajch, and the improved instrument was unveiled at an inaugural concert by . "The sound is clearer, even more lively, thanks to the new old-fashioned bellows," Novenko told Prague Post. "The organ master needs to think in the spirit of the original organ builder. It's a solitary job, much more difficult than building a new organ."