Slayer began writing lyrics for a new album prior to their appearance at the 1999 Ozzfest. However, every three to four months the band was distracted by commitments to Ozzfest, and worldwide "Tattoo the Earth" tour with Slipknot. Guitarist Jeff Hanneman later admitted "that was the last break. Then we got our shit together." The band's longtime producer, Rick Rubin, was too busy to work with Slayer, and felt "burned out"—unable to create intense music. Araya and King had similar feelings about Rubin, and King remarked he "wanted to work with someone into the heavy-music scene, and Rubin's not anymore. I wanted somebody who knows what's hot, knows what's selling, knows the new techniques, and will keep me on my toes." Rubin recommended two producers, although the first producer was not going to work out personality-wise according to Hanneman. The band gave second candidate, Matt Hyde, a trial on the song "Bloodline", which appeared in the movie Dracula 2000. The band was pleased with Hyde's work on "Bloodline" and hired him to produce the entire album.
God Hates Us All was to be recorded in a Hollywood studio; however, the band relocated to Vancouver, British Columbia due to the availability of cheaper studio time. Hyde recommended a studio to the band—The Warehouse Studio (owned by Bryan Adams) as he had previously worked there. The studio was altered to make it "feel like home" for Slayer; as opposed to the setting for, in King's words, the "lightweight Canadian pop singer". This consisted of adding incense burners, candles, dimmed lights and pornography on the walls. Two banner flags of two middle fingers were also hung up. Vocalist Tom Araya says "that was basically the attitude of Slayer in the studio. We had a red devil head on one of the speakers. We had a skull on another. That's the kind of shit we put up. Spooky stuff that makes you feel at home."
Hyde used the digital audio workstation Pro Tools during the engineering, production, and audio mixing stages of the album. Slayer members wanted to keep the use of computer effects to a minimum, only to include a small amount of delay and distortion. As with previous recordings, the drum tracks were recorded first. Drummer Paul Bostaph follows a simple rule suggested by Rubin when in the studio: "The perfect take is the one that felt like it was going to fall apart but never did." Seven-string guitars were used on the tracks "Scarstruck" and "Here Comes the Pain," the first time Slayer had done so. King was at the B.C. Rich guitar company (manufacturer of his signature model, the KKV) and decided to borrow a seven string guitar. After writing one song, King ordered a seven string as he thought "there's no point having one tuning for just one song," so he wrote another, going on to comment "you don't have to be good to make up a seven-string riff." The album features two songs on seven string guitars, four songs with guitars tuned to Drop-B and all other songs in C# Standard.