Denise Sullivan of Allmusic praised "Mysterious Ways", saying it is "structured like a gospel chant" and "maintains its deep groove with the assistance of some chunky guitar riffing, a persistent percussive beat, and what sound like spontaneous vocal bursts by Bono in the R&B tradition". In a review of the album's 20th anniversary reissue, Kit O'Toole of the "Seattle Post-Intelligencer" said "Mysterious Ways" exemplified the evolution of the band's sound. In her opinion, despite the song's sonic flourishes, "this departure does not jar longtime fans, as it retains the core of U2—loud, swooping rock guitar, a huge voice, and powerful drums. Quite simply, it's a textbook example of how artists can alter their sound without compromising their essential beliefs."