By the middle of the 19th century, the Frankfurt Jewish community was dominated by the Reform movement. As result, the community closed the mikveh and refused financial support to the Orthodox community. In response, the Orthodox Jews withdrew from the larger community and formed the Religiongesellschaft, appointed R. Samson Raphael Hirsch their rabbi, and began a 25-year struggle for official autonomy. In July 1876, the Orthodox community was officially recognized by the State. The Reform-led general Jewish community offered to restore all the support it had previously rescinded, but the group led by Hirsch refused the offer. To help settle the controversy, Orthodox community members turned to R. Bamberger. Contrary to their expectations, R. Bamberger ruled that it was unnecessary to secede from the Reform-led community since it was providing for all of the needs of the Orthodox. Throughout the ensuing year, R. Hirsch and R. Bamberger engaged in a public, somewhat acrimonious polemic. The central issue of their argument was whether or not the Reform Jews were to be considered heretics. R. Hirsch said yes, while R. Bamberger said no. In the end, only a small portion of the entire Orthodox community seceded with R. Hirsch from the larger Reform-led community. Ironically, R. Hirsch, who represented the more modern Orthodox perspective, became the forerunner of 20th century ultra-Orthodox communities who try to cut themselves off as much as possible from the surrounding non-Orthodox and secular Jewish community. Despite his religious conservatism, R. Bamberger's position became the basis for modern Orthodox openness and acceptance of the surrounding non-Orthodox and secular Jewish community.

The "Wuerzburger Rav," as he was called, was one of the last great German-style talmudists, and his literary work was chiefly devoted to subjects of practical halakhah; Melekhet Shamayim (on the writing of Torah Scrolls etc., 1860); Amirah le-Veit Ya'akov (laws of interest to women, originally German in Hebrew characters, 1858); Moreh la-Zovehim (handbooks for shohatim, 1864); Nahalei Devash (on the law of halizah, 1867). R. Bamberger also wrote a commentary on R. Isaac ibn Ghayyat's halakhic compendium (Sha'arei Simhah, 2 pts., 1861–62) and a treatise on the Al Tikrei formula in Talmud and Midrash (Korei be-Emet, 2 pts., 1871–78). His responsa appeared posthumously in Zekher Simhah (1925), Neti'ah shel Simhah (1928), and Yad ha-Levi (1965), all published by one or another of his descendants. Together with A. Adler and M. Lehmann, R. Bamberger published a German translation of the Pentateuch (1873) on behalf of the Orthodox-Israelitische Bibelanstalt to counter L. Philippson's Bible translation, against which he had published a polemical pamphlet (1860).