Guitarist Kerry King wrote roughly 80% of the lyrics, adopting a different approach from earlier recordings by including prevalent themes such as religion, murder, revenge, and self-control. Limiting the lyrics to topics which everyone could relate to, King wished to explore more in depth, realistic subject matter. The band experimented musically by recording two songs with seven-string guitars, and a further two with drop B tunings. The album's release was delayed due to the graphic nature of its artwork for which slip covers were created to cover the original artwork, difficulties encountered during audio mixing, and the change of distributor by the band's record label during the release period.
God Hates Us All was to be recorded in a Hollywood studio; however, the band relocated to Vancouver, Canada 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 drawing a chalked-out crime-scene of a body on the floor and adding incense burners, candles, dimmed lights, skulls, and pornography on the walls. Two banner flags of two middle fingers were also hung up, and the first door in the studio had a Misfits skull which had "Eat a bag" written on it. 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 "Warzone" 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." Four songs are in drop B tuning and the remainder of the album is in C sharp.
I definitely wanted to put more realism in it, more depth. God Hates Us All isn't an anti-Christian line as much as it's an idea I think a lot of people can relate to on a daily basis. One day you're living your life, and then you're hit by a car or your dog dies, so you feel like, "God really hates me today."
In the documentary Metal: A Headbanger's Journey, Araya went on saying "God doesn't hate... [but] it's a great fucking title."
The song "Threshold" deals with reaching your limit with a person in a situation where you’re about to break — about to blow-up as they get "under your skin" and "Cast Down" is about a fallen Angel who resorts to drugs. "God Send Death" is based on a creature that killed in the past, while "Deviance" takes up the idea of killing people for pleasure, both songs were written by Hanneman. Having read several books on serial killers, Hanneman put thought into the lyrics and came to the conclusion he could only kill someone if they really "pissed him off", unable to kill someone he did not know just for power. He later remarked that he was trying to get into that person's mind; "why do they get off on it? Without being angry, just killing for the sake of killing and getting off on it. I just wanted to get into that mindset."
While other members went to local pubs, Araya spent his free hours reading factual books regarding serial killers, including Gordon Burn's Happy Like Murderers: The Story of Fred and Rosemary West. Araya was seeking inspiration, and aimed to sound convincing while singing the lyrics, avoiding himself to sound like a gimmick. Araya sang the lyrics more "over-the-top" than done on previous albums, as King's writing style is more "aggro." This resulted in Kerrang! reviewer Jason Arnopp describing the album's lyrics as "so packed with foul and abusive language that it sounds as if D-12 and the Sopranos family were going head-to-head in a celebrity swearathon."
God Hates Us All was originally intended to be named Soundtrack to the Apocalypse. However, Araya suggested that the title would be a better used for a box set, which the band released in 2003. The phrase God Hates Us All originates from the song "Disciple", during which the line is repeated over the chorus. The lyrics are in reference to God's allowance of acts such as suicide and terrorism, while seemingly doing nothing to prevent them. A member of the heavy metal band Pantera suggested using "God Hates Us All" for a shirt design after King played the song to the band. King agreed, although he thought the phrase would have more impact as the album title.
The original album cover depicts a Bible spiked with nails, covered in blood and "Slayer" burnt across it, while the liner notes feature Bible verses crossed out with a black marker. The idea was suggested by the band's record company, although King wished to have more time to develop a better cover. King thought the idea "represents a record company with absolutely no idea what the fuck they were going to do", and said that the effort "looked like a seventh grader defaced the Bible." King's concept for the cover was to insert nails in a shape of a pentagram, and have the nails miss keywords in Bible verses so it appeared as if it had been created by a sociopath who knew where every word appears. A slip insert was created to be placed in front of the covers in stores.
God Hates us All received mixed reviews from music critics. Kerrang!'s Jason Arnopp described the album as "easily Slayer's most convincing collection since Seasons in the Abyss," awarding the album five out of five. Rolling Stone's Rob Kemp wrote the record was "Slayer's most brutal record since 1986's immortal (or undead) Reign in Blood," describing the music as "galloping double-bass-drum salvos" which "switch on a dime to furious double-time pummeling, as ominous power chords and jagged shred solos slice and dice with Formula One precision." Kemp awarded the album three and a half out of five. Allmusic reviewer Jason Birchmeier commented that "nearly 20 years into their evolution, Slayer have abandoned the extravagancies and accessibility of their late-'80s/early-'90s work and returned to perfect the raw approach of their early years. A near flawless album," and that Araya's performance possibly makes "the most exhausting Slayer album yet."
However, not all critics were impressed with the album. Blabbermouth.net reviewer Borivoj Krgin dismissively labeled the album as "another failure on the band's part to take the initiative and reinvent themselves." Krgin described King as “the weaker and less inventive of the two main songwriters” (King and Hanneman), feeling the album followed “a familiar direction that almost always sounds tired and forced” as a result of King being the album's main songwriter. Krgin also singled out Araya for criticism, and called the vocalist a "hollow shell of his former self, boasting a singing style that is monotonous, devoid of creativity and at times virtually unlistenable." Krgin awarded the record 6 out of 10, and ended the review by observing that "Slayer's rapidly diminishing record sales (Diabolus In Musica has shifted less than 300,000 copies in the US compared to 600–700,000+) as a sign that the band is in dire need of a new lease on life."
The song "Disciple" received a Grammy Award nomination for "Best Metal Performance" at the 44th Grammy Awards, the band's first nomination. The members cared neither about the nomination nor the award ceremony, and although they did not expect to win, thought it was "cool" to be nominated. The ceremony took place on February 27, 2002, with Tool winning the award for their song "Schism".
Following the tour, the band continued their search for a permanent drummer, and sought solicitation via demo tape and snail mail. Interested fans sent video recordings of renditions of the songs "Disciple," "God Send Death," "Stain of Mind," "Angel of Death," "Postmortem/Raining Blood," "South of Heaven," "War Ensemble," and "Seasons in the Abyss"; complete with résumés. The band listened to hundreds of demo tapes, and created a "good pile" and "ungood pile," though the "ungood" was much larger. Those whose performances the band were pleased with were offered an audition in Dallas, San Francisco or Peoria, Illinois; many applicants, however, were unable to attend due to flight costs. The band auditioned roughly two to three drummers a day, and their top choice was one of Lombardo's recommendations. However, the band ultimately returned to Lombardo after deciding that they could not find a drummer who suited the job; Lombardo re-joined Slayer and attended music festivals worldwide to promote God Hates Us All and record drums on the 2006 album Christ Illusion.