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' yeshiva. At the same time his younger son, Wolf, presented himself as a Shabbatean prophet, with the result that the yeshiva was closed.

מעבר לשער: הקדמת המעתיק, ר' אורי ב"ר יהודא ליב. בדף טו, א מעיר "המעתיק" ומזכיר את ספרו של ר' יהונתן "בני אהובה", "שלא נדפס עדיין, וישנו תחת ידי בכתיבת ידיו" ("בני אהובה נדפס בפראג תקע"ט). הדברים נכתבו לפני שנדפס "בני אהובה", אך איו זה אומר ש"תפארת יהונתן" נדפס לפני שנת תקע"ט. בטופס שבספריית ג'וז קוליג' בלונדון נוספו אחרי שמו של המביא לדפוס שתי שורות: "נכד הרב... מנחם מענדל זאלקוויר מ"מ ומ"צ דק"ק בראד... בן... מו"ה אפרים זלמן לוקביר מ"מ ומ"צ דק"ק זאלקווי".