Confusion Is Sex was recorded by Wharton Tiers in his Chelsea studio (which he had set up in the basement of a building where he worked as superintendent). It was mostly recorded during Jim Sclavunos' brief tenure as drummer for the band, and he appears on drums for most of the album. Frustrated by the unconventional recording situation in Tiers' studio and generally not clicking with the band musically, Sclavunos was ejected and Bob Bert was invited back, who recorded drums for "Making the Nature Scene". Bert appears on this track and the live Stooges cover "I Wanna Be Your Dog" on the album. Confusion Is Sex is the only Sonic Youth album on which guitarist Lee Ranaldo plays bass, specifically on the song "Protect Me You".
The track "Lee Is Free" was recorded on two tape recorders by Lee Ranaldo solo at home. The track "Confusion Is Next" contains lyrics sung twice by Moore. The first part of the song is slow and the second chapter everything is played twice the speed. The title was later used for the book by Alec Foege.
This album features a guitar sound often reminiscent of clocks and bells. This is created by using prepared guitars with screwdrivers stuck between the fretboard and the strings. Notable songs where Ranaldo and Moore used this 3rd bridge technique are "Protect Me You", "The World Looks Red" and "Lee Is Free". The band also used this technique on their debut EP. On later albums the group abandoned the technique and shifted to a deeper focus on alternate tunings. The group got the idea of the prepared guitar techniques from their experiences with Glenn Branca, who also published this album on his label Neutral Records.