Rabbi Yehonatan Eybeschutz was born around 5454 (1694) according to recent research (other sources give 1690), in Pinczów, Poland, according to most of his biographers (others say Kraków). His mother Sheindel was the daughter of Rabbi Moshe Yitzchak Yehuda Leib Zuntz; his father, Rabbi Nosson Nota, rabbi of Eibenschütz in Moravia, descended from Rabbi Nosson Spira, author of the Megaleh Amukot. A child prodigy, he was called "the illui of Pinczów," and lost both parents at a young age.

Orphaned, he grew up in Prossnitz in the home of Rabbi Meir Eisenstadt, the Maharam Ash, whom he regarded as his first teacher, then studied in Holleschau under Rabbi Eliezer HaLevi Ettinger before living in Vienna. In 5470 (1710) he married Elkele, daughter of Rabbi Moshe Yitzchak Spira.

Settling in Prague, in 5474 (1714) he became the community's preacher and head of its great yeshiva, serving for about twenty-five years; after the death of Rabbi David Oppenheim (1736) he headed the rabbinical court. In 5501 (1741) he was elected rabbi of Metz, and in 5510 (1750) rabbi of the "Three Communities" of Altona, Hamburg and Wandsbek.

He also engaged in Kabbalah and wrote amulets, which led Rabbi Yaakov Emden to accuse him of Sabbateanism and sparked a long controversy. Most rabbis of his generation supported him and the Hamburg Senate ruled in his favor, yet the dispute prevented his appointment as rabbi of Prague.

Works: Kereti uPeleti on Shulchan Aruch Yoreh De'ah, Urim veTumim on Choshen Mishpat, the sermons Yaarot Devash, Tiferet Yehonatan on the Torah, and Luchot Edut, in which he answers the charges against him. He passed away in Altona on 21 Elul 5524 (18 September 1764) and was buried in the Jewish cemetery of Altona.