This is the first album to feature bassist Hunter Burgan, although he was not a permanent member at the time as well as the final album to feature founding guitarist Mark Stopholese. Future band member Jade Puget performed backing vocals for the album as well, making Shut Your Mouth and Open Your Eyes the first AFI album the band's current members collaborated in. Nick 13 from American rock band Tiger Army is featured in the track "A Single Second", performing vocals in the chorus of the song.
A music video directed by Darren Doane and Ken Daurio was made for the track "Third Season." It features the band themselves sitting in a suburban town while a slew of children chase an ice cream truck.
The inner-edge of the album's CD case reveals the hidden message "A Fire Inside", a lyric from the introductory track "Keeping Out of Direct Sunlight". This is the first album to quote the phrase, which eventually became AFI's permanent acronym.