Disappointed with life in New York, in 1999 Odzer returned to Goa, where some of the remaining old-time hippies disliked her because of the publicity her book had brought to the scene. She died there in 2001. A good friend of hers who had been corresponding with Odzer during her final stay in India, "Cookie" (with whom she recorded The Groupies), reports that Odzer's doctor (who had been away when she died) said she probably died of a stroke related to very high cholesterol and serious circulatory problems that she was being treated for during her final year, and that her body had been cremated after a small service. But a researcher, Arun Saldanha, who interviewed members of the Goa community about Odzer, reports being told by a psychiatrist at the Goa Medical College some ten months after her death that her body had lain unclaimed in a morgue in Mapusa for more than a month until finally she had been buried in Mapusa without a funeral, and that she had had AIDS. Saldanha also reports having seen Odzer use cocaine during an interview he had with her sometime before her death.
The 2002 documentary Last Hippie Standing by Marcus Robbin covered the Goa scene and featured some of Cleo Odzer's old super-8 footage from the 1970s. She was interviewed by Robbins for the film in Goa shortly before her death, and said: "I don't know what the future brings, but I know what I don't want: New York is what I don't want, that culture is what I don't want; it's not right. I don't know what is right. I don't think our old life was right. I don't see a new culture that is right, but we have to continue trying, that's the best we can do, that's the best any of us can do, to keep trying. To make something that is peaceful for everybody, that makes people happy, that is fair to everybody. And that's all I want". The film was dedicated to her memory.