Jonathan Eibeschutz was born at the end of the 17th century in Poland. He was a child prodigy in Talmud. He settled in Prague in 1715 and became head of the yeshivah and a famous preacher. In Prague, Eibeschutzhe had many contacts with priests and the intelligentsia, debating religious topics and matters of faith with them. He became friendly with Cardinal Hassebauer and also discussed religious questions with him. Through the help of the cardinal, Eibeschutz received permission to print the Talmud with the omission of all passages contradicting the principles of Christianity. This angered the rabbis of Prague, and they revoked the printing license.
The people of Prague held Eybeschuetz in high esteem and he was considered second only to David Oppenheim. In 1725, he was among the Prague rabbis who excommunicated the Shabbatean sect. In 1736, Eibeschutz was appointed dayyan of Prague. He became rabbi of Metz in 1741. In 1750, he was elected rabbi of the "Three Communities:" Altona, Hamburg, and Wandsbek Eibeschutz was considered a great preacher, and his pilpul approach to Talmud was highly honored.
In 1751, a huge controversy broke out between Eibeschutz and Jacob Emden, which affected most of German Jewry. Like Eibeschutz, Emden was a great talmudist, He had applied for the rabbinic post where Eibeschutz served. Eibeschutz had apparently written some amulets while rabbi of Metz. Emden analyzed them and declared that they were Shabbatean. A huge uproar ensued, and Emden had to flee to Amsterdam for a while. Eibeschutz denied the accusation, which in any case could not be proved with certainty.
The majority of the greatest rabbis in Poland, Moravia, and Bohemia, as well as the leaders of the Three Communities supported him, either because the accusation was utterly incredible, or because they feared the repercussions of a scandal if their leading rabbi was found to be a Shabbatean.
Emden disregarded these considerations vehemently. He fought his opponent and his numerous supporters by writing numerous books and pamphlets. The controversy was so divisive that both sides appealed to the authorities in Hamburg and the government of Denmark for a judicial ruling. The king favored Eibeschutz and ordered new elections, which resulted in his reappointment.
The controversy just wouldn't go away, however. After his reelection as rabbi of the Three Communities, some rabbis of Frankfurt, Amsterdam, and Metz challenged him to appear before them to reply to the suspicions raised against him. Eibeschutz 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 Eibeschutz' yeshivah. At the same time his younger son, Wolf, presented himself as a Shabbatean prophet, with the result that the yeshivah was closed.
The great bitterness this controversy stemmed precisely from his being recognized as a true master of the Torah. It was hard to believe that a man who had himself signed a cherem against the Shabbateans could have secretly held their beliefs. Scholars continue to argue both sides of the question.
Sources: Gates of Jewish Heritage