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 a 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. Bert appears on "Making the Nature Scene and the live Stooges cover "I Wanna Be Your Dog". Confusion Is Sex is the only Sonic Youth album on which guitarist Lee Ranaldo plays bass, specifically on the song "Protect Me You".
This album features a guitar sound often reminiscent of clocks and bells, 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 issued this album on his label Neutral.