The album was recorded in Los Angeles, California with Reign in Blood producer Rick Rubin. PopMatters reviewer Adrien Begrand observed that Rubin's production "shoves [Dave] Lombardo's drumming right up front in the mix". Guitarist Jeff Hanneman has since said that South of Heaven was the only album the band members discussed before writing the music. Aware that they "couldn't top Reign in Blood", and that whatever they recorded would be "compared to that album", he believed they "had to slow down", something Slayer had never done on albums before, or since. Guitarist Kerry King cited the need to "keep people guessing" as another reason for the musical shift. "In order to contrast the aggressive assault put forth on Reign in Blood, Slayer consciously slowed down the tempo of the album as a whole", according to Slayer's official biography. "They also added elements like undistorted guitars and toned-down vocal styles not heard on previous albums."
King has since been critical of his performance, which he describes as his "most lackluster". King attributes this to the fact he had recently married, and moved to Phoenix, Arizona. Describing himself as "probably the odd man out at that point", he stated he "didn't participate as much because of that". Hanneman said: "We go through dry spells sometimes, but the good thing about having two guitar players that can write music is that you are never gonna go without. I guess at that time, Kerry was hitting a dry spell." King has also been critical of the album in general, describing it as one of his least favorite Slayer albums. He feels vocalist Tom Araya moved too far away from his regular vocal style, and "added too much singing". Drummer Dave Lombardo has since observed: "There was fire on all the records, but it started dimming when South of Heaven came into the picture. And that's me personally. Again, I was probably wanting something else."
Judas Priest's "Dissident Aggressor" is the first cover version to appear on a Slayer studio album. The song was chosen due to its war-themed lyrics. Hanneman described the track as "more just like one of those odd songs that a lot of people didn't know, but it was a favorite of Kerry and I, so we just picked that one". Meanwhile, "Cleanse the Soul" has been heavily criticized by King who said that he hates the track: "That's one of the black marks in our history, in my book. I just fucking think it's horrible. [Laughs] I hate the opening riff. It's what we call a 'happy riff.' It's just like 'la-lala-la-la-la.' I can't see myself playing it, but after that, where it gets heavier, I like that section. If we ever did a medley, I'd put part of that in there." The Slayer boxset Soundtrack to the Apocalypse featured, along with four songs of the album, an early version of the title track, recorded at Hanneman's home.