Soundgarden began work on the album about two months after finishing its stint on the 1992 Lollapalooza tour. The individual band members would work on material on their own and then bring in demos to which the other members of the band would contribute. Frontman Chris Cornell said that the band members allowed each other more freedom than on past records. Thayil observed that even though the band spent as much time writing and arranging as it had on previous albums, it spent a lot more time working on recording the songs. After two albums with producer Terry Date, the band decided to seek another collaborator, as guitarist Kim Thayil said, "We just thought we'd go for a change." Eventually they settled on producer Michael Beinhorn, who "didn't have his own trademark sound which he was trying to tack on to Soundgarden" and had ideas the band approved.
The album's recording sessions took place from July 1993 to September 1993 at Bad Animals Studio in Seattle, Washington, as according to Cornell "there was never a decent studio in Seattle and now there's one with a Neve console, so it seemed obvious to use it". Bad Animals' resident engineer Adam Kasper, who went on to produce Soundgarden's following albums, assisted Beinhorn on the recording process. Soundgarden took the approach of recording one song at a time. The drum and bass parts were recorded first for each song, and then Cornell and Thayil would lay down their parts over top. Cornell said that getting to know Beinhorn contributed to the length of time Soundgarden spent working on the album. The band spent time experimenting with different drum and guitar sounds, as well as utilizing techniques such as layering, resulting in an expansive production sound. Cornell said, "Michael Beinhorn was so into sounds. He was so, almost, anal about it, that it took the piss out of us a lot of the time ... By the time you get the sounds that you want to record the song, you're sick and tired of playing it." Beinhorn tried to add many of his preferred musicians to mold the band's sound, in what Billboard described as "weaning the band from brute force, giving it the impetus to invest in a more subtle power". For instance, prior to recording the vocals of "Black Hole Sun", Beinhorn made Cornell listen to Frank Sinatra.
Superunknown lasts for 15 songs clocking on approximately 70 minutes because according to Cornell, "we didn't really want to argue over what should be cut". Soundgarden took a break in the middle of recording to open for Neil Young on a ten-day tour of the United States. The band then brought in Brendan O'Brien to mix the album, as Beinhorn felt the band needed "a fresh pair of ears"; O'Brien had come recommended by Pearl Jam guitarist Stone Gossard. Thayil called the mixing process "very painless", and bassist Ben Shepherd said it was "the fastest part of the record".