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 R. 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).

His position in the Three Communities, however, was undermined when the dispute broke out concerning his suspected leanings toward Shabbateanism. This controversy accompanied R. Eybeschuetz throughout his life, and the quarrel had repercussions in every community from Holland to Poland. His main opponent was R. Jacob Emden, also a famous talmudist and a potential rival in the candidature to the rabbinate of the Three Communities. The quarrel developed into a great public dispute which divided the rabbis of the day. While most of the German rabbis opposed R. Eybeschuetz, his support came from the rabbis of Poland and Moravia. A fruitless attempt at mediation was made by R. Ezekiel Landau, rabbi of Prague. Most of R. Eybeschuetz' own community was loyal to him and confidently accepted his refutation of the charges made by his opponent, but dissension reached such a pitch that both sides appealed to the authorities in Hamburg and the government of Denmark for a judicial ruling. The king favored R. Eybeschuetz and ordered new elections, which resulted in his reappointment. After his reelection as rabbi of the Three Communities, some rabbis of Frankfort, Amsterdam, and Metz challenged him to appear before them to reply to the suspicions raised against him. R. Eybeschuetz refused, and when the matter was brought before the Council of the Four Lands in 1753, the council issued a ruling in his favor. In 1760 the quarrel broke out once more when some Shabbatean elements were discovered among the students of R. Eybeschuetz' yeshivah. At the same time his younger son, Wolf, presented himself as a Shabbatean prophet, with the result that the yeshivah was closed.

חלק א: סימנים א-עב. מעבר לשער הקדמת המביא לדפוס, ר' ישראל ב"ר נתן נטע אייבשיץ, נכד המחבר. חלק א: דף לג-מט,א (בין סי' כה-כו): "קיצור תקפו כהן מהש"ך", עם אורים ותומים. חלק ב: סי' עג-קנב. עם שער מיוחד ועליו הקדמת ר' ישראל ב"ר נתן נטע, שסידר גם את המפתח בסוף הספר. חלק ב: דף רלא,ב - רמג,א (בין סי' פב-פג): "קיצור כללי מגו מכה"ג" [מכנסת הגדולה, מאת ר' חיים בנבנשתי], עם ביאורים.