Everlast wrote the song while recovering from a major heart attack that he had suffered in February 1998 (directly after he completed recording his first solo album, Whitey Ford Sings the Blues). He has referred to it as "one of the most personal songs I ever wrote", stating that the song was "kind of all about hope, but it's coming from a really dark place you know, so... and really questioning a lot of your beliefs, and affirming, you know, stuff in your soul."[2] Everlast converted to Islam in 1996, and the end of the song contains the words "La ilaha illa Allah", ("There is no God but God" in Arabic), the first part of the Shahada, the Islamic profession of faith.
Santana called Everlast in 1998, asking him if he could contribute a song for Supernatural, and Everlast suggested "Put Your Lights On". According to Everlast, Santana loved the song, and "from then on everything went very fast." Everlast has stated that he was unsure whether to include the Arabic-language portion in the recorded song, because "I did not want to sell Allah's words", but that Santana insisted that they be included.[3]