Flesh was shot by Paul Morrissey while Andy was recuperating from his gunshot wounds. Warhol never actually attended any of the filming.
Previously, some of the Factory crowd had been invited to appear in in Midnight Cowboy for a party scene which was being filmed, but spent much of their time just waiting around on the set with the extras. Both Paul and Joe were there and came up with an idea for a film that would be about a boxer, incorporating some of the stories that Joe told Paul about his life or the people he had met on the street.