Gafni's 2003 book, Mystery of Love, further established his reputation as a provocative thinker on the subjects of eros, sexuality, and relationships.

Despite Gafni's denials and attempts to frame the relationships as consensual,[14][15] the allegations led to significant fallout, including the return of his rabbinical ordination to Rabbi Shlomo Riskin.

Despite ongoing allegations and public disavowals from former supporters, Gafni has persisted in his spiritual and philosophical work, publishing books such as Radical Kabbalah and A Return to Eros.

[1] Gafni also did a series of weekly television spots with Israeli comedian Gil Kopatch on biblical wisdom for everyday life.

[1][19] Gafni described himself and his students as "dual citizens" of both their native traditional religion and the broader themes of "world spirituality".

[1] He wrote an essay, "A Hundred Blasts Shatter the Somber Silence", which appeared in Arthur Kurzweil's Best Jewish Writing 2003.

[16] The Bayit Hadash co-founders and other prominent leaders expressed that they felt betrayed by how deeply Gafni had misled them as well as regret for having supported him.

[citation needed] At the Center, Gafni and Ken Wilber founded a Wisdom Council to envision a spirituality based on Integral Principles.

[35] The Wisdom Council, which is no longer active[citation needed], included members such as Gafni, Wilber, Tony Robbins, Warren Farrell, Lori Galperin, Sally Kempton.

[38] Tami Simon, CEO of Sounds True, canceled her planned publication of Gafni's book, Your Unique Self, and issued a statement denouncing him.

"[49] Within two weeks of the publication of the piece in The Times of Israel, Sara Kabakov revealed in The Forward that she was the other formerly unnamed teenage girl who had been abused by Gafni in the early 1980s, beginning when she was thirteen years old.

Gafni wrote: "This group of protestors, led by many of my competing adversaries, is using Mackey as a platform to continue their smear campaign designed to destroy my reputation and career.

"[55] Mackey issued a public statement, saying: "While combating sexual abuse or harassment is essential and something I fully support, so is providing a fair forum for those being wrongly accused.

"[55] John Mackey rejected the demands that he should distance himself from Gafni with the following statement: "Loyalty and the presumption of innocence are important values to me, so I will not join those who are condemning him.

"[56][57] In April 2016 it was learned that John Mackey had stepped down, as he had completed his role as chairman of the Center for Integral Wisdom board.

[58] In February 2017, the National Coalition for Men published an article by Gafni in which he defended himself, calling the allegations "a long-standing smear campaign".

[15] In 2020, Kabakov and Mitzner filed suit against both Gafni and Yeshiva University under the recently passed New York Child Victims Act.

[26][59][60] In 2017, Gafni published A Return to Eros: The Radical Experience of Being Fully Alive, co-authored with Kristina Kincaid.

[61] Gafni expresses that "the sexual is the ultimate Spiritual Master" and has written "I was convinced from an early age that religion had lost what I believed must have been its original erotic vitality.