In 1851 Hildesheimer was appointed rabbi of the Austro-Hungarian community of Eisenstadt; there he reorganized the educational system and established a yeshivah, where secular studies were included in the curriculum. The yeshivah was highly successful, and students came there from all over Europe. However, the great majority of Orthodox Hungarian rabbis bitterly opposed his modernism and the institution he created. In 1869 Hildesheimer accepted a call from Berlin to become rabbi of the newly founded Orthodox congregation, Adass Jisroel. In 1873 he established a rabbinical seminary which later became the central institution for the training of Orthodox rabbis in Europe. Hildesheimer shared with S. R. Hirsch the leadership of the Orthodox Jewish community of Germany. He was an active worker on behalf of stricken Jewish communities throughout the world. Throughout his life, he was an enthusiastic supporter of Palestine Jewry and the building of the yishuv. The Battei Mahaseh dwellings in the Old City of Jerusalem were erected on his initiative. In 1872 he founded a Palaestina Verein with the object of raising the educational and vocational standards of Jerusalem Jews, particularly by the establishment in 1879 of an orphanage. This drew on his head the bitter antagonism of the ultra-Orthodox old yishuv, which placed him under a ban (herem). Hildesheimer supported the Hovevei Zion and the colonization movement.

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). Bamberger also wrote a commentary on 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, Bamberger published a German translation of the Pentateuch (1873, 19137) on behalf of the Orthodox-Israelitische Bibelanstalt to counter L. Philippson's Bible translation, against which he had published a polemical pamphlet (1860).

הסכמה: ר' יעקב ב"ר אהרן עטטלינגער, אלטאנא, ה' אדר-ב תרי"ג.