Slayer's previous album, Show No Mercy, had sold over 40,000 copies worldwide and the band were performing the songs "Chemical Warfare" and "Captor of Sin" live, which made producer Brian Slagel want to release an EP. The album was recorded in Hollywood with sound engineer Bill Metoyer, in a studio with no carpet which was a problem while recording the drums. Slagel was acting as executive producer. Metoyer is Christian and the lyrics from Show No Mercy did not bother him. However, the first words Araya sang when recording Haunting the Chapel were "The holy cross, symbol of lies, intimidates the lives of Christian born", and other anti-religious lyrics; Metoyer thought he would go to Hell for his part in recording the lyrics. These lyrical themes were inspired by the band Venom, who influenced King and was also into the Satanic image.
Slayer drummer Dave Lombardo set his drum kit on the concrete and the kit went "all over the place" while playing. Lombardo asked Gene Hoglan to hold his kit together, while recording "Chemical Warfare", with Hoglan thinking, "I hope he does this in one or two takes, because this is rough." Hoglan was coaching Lombardo how to use double-bass drums to improve his drumming ability and speed; Lombardo asserts Hoglan was "an amazing double-bass player even back then", although Hoglan played double bass since a short time then. Eddy Schreyer provided audio mastering and digital remastering, with the cover art design created by Vince Gutierrez. Haunting the Chapel was darker and more thrash-oriented than Show No Mercy, and laid the groundwork for the future direction in the band's sound.