He is a co-founder and director of Eshel, a support, education and advocacy organization for orthodox LGBT Jews that saves lives and families.

From 1996 to 1998 he spent two years as a Jerusalem Fellow with the Mandel Institute,[9]: 11  studying educational policy issues and researching rabbinic attitudes toward homosexuality.

[12] Greenberg officiating at a civil marriage between two men in the United States,[12] first reported by +972 Magazine on November 11, 2011,[13][unreliable source] attracted controversy and was misunderstood and rejected by many within the Jewish community.

In a 2001 article "Between Intermarriage and Conversion: Finding a Middle Way" published in CLAL, Greenberg proposes using the rabbinic concept of ger toshav, (resident alien), to provide an accepted place for non-Jewish partners of intermarried couples, allowing them to experience "the joys of living in a Jewish home without insisting on conversion".

As a marriage of a Jew and a ger toshav would not be legitimate under halachic law, Greenberg suggests using "cultural creativity" to find "new rituals that partake of Jewish resources and speak honestly about what is actually happening", the same as for gay couples, where in his opinion "kiddushin, the traditional ritual for the Jewish wedding, simply doesn't apply".

[19] In 2004 Greenberg's book, Wrestling with God and Men: Homosexuality in the Jewish Tradition was published, meeting with critical acclaim.

According to this analysis the verse prohibits one, and only one, sexual practice between men, namely, anal intercourse, and speaks specifically to the active partner.

"[9]: 81  In Greenberg's reading "the verse prohibits the kind of sex between men that is designed to effect the power and mastery of the penetrator.

In Tendler's opinion "it is very sad that an individual who attended our yeshiva sunk to the depths of what we consider a depraved society" and called Greenberg "a Reform rabbi".

What Rabbi Greenberg apparently believes is that elements of the Jewish religious tradition are negotiable, that the Torah, like a Hollywood script, can be sent back for a rewrite.

"[25][unreliable source] In his review of Wrestling with God and Men for the Edah Journal, Rabbi Asher Lopatin affirmed Greenberg's "importance as a voice within the Orthodox community", and calls him "a brilliant, thoughtful and courageous rabbi" and his book "a brilliant work of creativity and research", he writes that "Wrestling with God and Man [sic], and Rabbi Greenberg's voice in this book fall outside the bounds of Orthodoxy" for three reasons: Because Greenberg "is not committing himself fully to Orthodoxy", because he "does not follow Orthodox methodology", and because he "is not sufficiently halakhically creative", not having "combined — in a novel way to be sure — [his] commitment to his homosexual identity and way of life with the binding nature of halakhah".

At the same time, Lopatin is confident, that "Greenberg can write the Orthodox book that will show us that he is committed to staying the long and difficult course of persuasion that Orthodoxy demands".