[2] Later in life, Ellis belonged to anti-Zionist synagogue Tzedek Chicago and befriended Rabbi Brant Rosen.

[4][5] In 1980 he received his doctorate in contemporary American Social and Religious Thought from Marquette University, where he again studied with William Miller.

Ellis's 2012 departure from Baylor was controversial as he and his supporters, including Cornel West, Rosemary Ruether, and Desmond Tutu, stated that a concerted effort was made to remove him due to his views on Israeli-Palestinian relations.

Baylor President Ken Starr and the university administration denied that Ellis was being targeted for his views but that the investigation had to do with privacy rules.

Ellis's writings deal with contemporary Judaism, Jewish liberation theology, Jewish-Arab relations, justice, and peace.

They are specifically concerned with Palestinian freedom, self-determination, and putting an end to Israeli occupation and war crimes.

[12][10] Among those who have commented positively on the work of Ellis are George McGovern, Noam Chomsky, Edward Said, Professor Susannah Heschel, Elliot Dorff, Cornel West and Desmond Tutu.