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 appeared 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".
Ranaldo recorded the track "Lee Is Free" solo at home on two tape recorders.