The song began as an improvisation called "Sick Puppy", with the band liking only the bass part that bassist Adam Clayton composed.

"Mysterious Ways" features a danceable beat, funky guitar hook, and conga-laden percussion, as well as mystical lyrics by Bono about romance and women.

"Mysterious Ways" reached the top ten on the singles charts of several countries, including Canada and the band's native Ireland, where it went to number one.

A music video for the song was filmed in Morocco and incorporated distorted images of Bono and a belly dancer, Morleigh Steinberg, who eventually married the Edge.

"Mysterious Ways" began as an improvised demo called "Sick Puppy" that the group recorded at STS Studios in Dublin,[4][5] as vocalist Bono, guitarist the Edge, and bassist Adam Clayton jammed over a drum machine.

Bono and a frustrated Lanois proceeded to argue intensely for over two hours, worrying sound engineer Joe O'Herlihy that a physical altercation would ensue.

"[7] The song "One", which proved to be breakthrough in the difficult recording sessions for Achtung Baby,[8] began after a moment of inspiration as the band worked on "Mysterious Ways".

[8] The band made progress on "Mysterious Ways" after the Edge began experimenting with the "Funk Wah" setting on a Korg A3 guitar effects unit and Bono told him to use it for the song.

[4] Much like they did for other songs from Achtung Baby, U2 continued to work on "Mysterious Ways" up to the recording deadline, adding a guitar overdub after the mix was already finished.

[10] Several different verses were written, but the Edge advocated those with a "nursery rhyme feel", such as "Johnny, take a walk with your sister in the moon / Let her pale light in to fill up the room".

Scholar Atara Stein, in an essay analysing U2 songs, describes "Mysterious Ways" as one of several Achtung Baby tracks that idealizes women and creates a false illusion of them.

Stein found religious meaning in the line "She moves in mysterious ways" and Bono's request to the woman to "Lift my days, light up my nights".

According to her, "Paradoxically, this process of idealization simultaneously elevates the woman as an idol to be worshipped while presenting her as a potentially dangerous force the singer must control.

When the single covers to "Even Better Than the Real Thing", "The Fly", "Who's Gonna Ride Your Wild Horses", and "Mysterious Ways" are arranged, a picture of the band members driving a Trabant is formed.

Rolling Stone called it a standout track among the new dance-influenced songs, praising its "ebullient hook and a guitar solo in which the Edge segues from one of his signature bursts of light into an insidious funk riff".

[16] Steve Morse of The Boston Globe called it an "exceptional love song ... with a rapturous chorus" and noted that even though Bono's vocals on the album differ significantly from his previous style, "Mysterious Ways" features him returning to his "yearning self".

[20] 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.