Bakshi-Doron was criticized by Haredi leaders for some of his halakhic (Jewish legal) decisions, and by the Reform movement for his position on assimilation.

In a 1996 sermon, Bakshi-Doron compared Reform Judaism to the biblical Zimri, who was killed by Phinehas for cohabitation with a Midianite woman.

[5] It was later seen as a historical precedent which led the way to the 2005 meeting between Chief Rabbis Shlomo Amar and Yona Metzger with the new Pope, Benedict XVI.

In 2000, while visiting the Jewish community in Singapore, Bakshi-Doron declared that he was in favor of giving away parts of East Jerusalem to the Palestinians as a way to end the Arab–Israeli conflict.

When Bakshi-Doron publicly told the farmers that they could rely on the sales, the Haredi newspaper Yated Ne'eman began to leak word that Eliashiv would delegitimize him and put him and his family in herem (ex-communication) if he refused to back down.

Despite the open support of Katsav and Israeli Prime Minister Ehud Barak, Bakshi-Doron ultimately succumbed to the pressure from Eliashiv.

Among those present at the conference were the former Archbishop of Canterbury George Carey, Rabbi Michael Melchior, the muftis of Bethlehem, and the Palestinian Authority police forces.

The attendees issued a joint agreement called the First Declaration of Alexandria of the Religious Leaders of the Holy Land, in which they denounced the ongoing violence in the Middle East.

[9] In 2004, Bakshi-Doron spoke out in favor of introducing civil marriage in Israel, saying that the law subjecting members of the different Millets to respective religious authorities had become irrelevant, and was now a source of division and hatred.

Bakshi-Doron received attention in January 2005 for attending the first World Congress of Imams and Rabbis for Peace in Brussels, Belgium.

[14] The ordinations, equivalent to higher education on Israel's public employees' salary scale, entitled recipients to bonuses of NIS2,000–4,000, then valued at an additional $530–$1,060 per month.

[18] At the age of 25[2] Bakshi-Doron married Esther, daughter of the previous Chief Rabbi of Akko, Shalom Lopes, with whom he had ten children.