Jonathan Eybeschutz (Yiddish: יהונתן אייבשיץ; c. 1690 – 18 September 1764) was a Rabbi, Talmudist, halakhist, and kabbalist, known for his conflict with Jacob Emden in the Emden–Eybeschutz Controversy. Eybeschutz served as the Dayan of Prague, and later as the Rabbi of the "Three Communities" of Altona, Hamburg, and Wandsbek.

Eybeschutz was born around 1690 in Kraków, Polish–Lithuanian Commonwealth (present-day Poland) to Rabbi Nosson Nota. Around 1700, Eybeschutz moved to Eibenschütz, Margraviate of Moravia (present-day Ivančice, Czech Republic) where his father had been appointed Rabbi.

Eybeschutz was a illui (Talmudic prodigy child); on his father's death, he studied in the yeshiva of Meir Eisenstadt in Prossnitz (now Prostějov), and then later in Holleschau (now Holešov in the Zlín Region). He also lived in Vienna for a short time. He married Elkele Spira, daughter of Isaac Spira-Fraenkel, and they lived in Hamburg for two years with Mordecai ha-Kohen, Elkele's maternal grandfather.

At eighteen, Eybeschutz was appointed rabbi of Bolesławiec, where he stayed for three years. Afterward, he settled in Prague in 1711 and became rosh yeshiva and a famous preacher. The people of Prague held Eybeschutz in high esteem, and he was considered second only to Chief Rabbi David Oppenheim.

In Prague, Eybeschutz received permission to print the Talmud, but with the omission of all passages contradicting the principles of Christianity, in consultation with Chief Rabbi David Oppenheim. Legends and rumors seeking to discredit the event said that he did this without the consultation of the Prague rabbis, and they revoked the printing license.

In 1724, in Prague, he was suspected of being a Sabbatean. Despite denouncing the Sabbatean movement on Yom Kippur, the accusations continued. Therefore, in 1736, Eybeschutz was only appointed dayan of Prague and not chief rabbi. He became rabbi of Metz in 1741 and, in 1750, was elected rabbi of the "Three Communities:" Altona, Hamburg, and Wandsbek.

In July 1725, the Ashkenazi beth din of Amsterdam issued a ban of ḥerem "excommunication" on Sabbateans (Hebrew: כַּת הַמַּאֲמִינִים, romanized: kaṯ hammaʾaminim, lit. 'Sect of the Believers'). Sabbatean writings found by the beth din at that time were attributed to Eybeschutz. In early September, similar excommunication proclamations were issued by the batei din of Frankfurt an der Oder and the triple community of Altona, Hamburg, and Wandsbeck. The three bans were printed and circulated in other European Jewish communities. Excerpts from the testimonies were printed by Jacob Emden in his Beth Jonatan haSofer, printed in Altona in 1762.

Katzenellenbogen was unwilling to attack Eybeschutz publicly, mentioning that "greater than him have fallen and crumbled" and that "there is nothing we can do to him." However, Katzenelenbogen stated that one of the texts found by the Amsterdam beth din, And I Came this Day unto the Fountain, was authored by Eybeschutz and declared that all copies of the work in circulation should be immediately burned. As a result of Eybeschutz and other rabbis in Prague formulating a new and distinct ḥerem against Sabbatianism shortly after the other bans were published, his reputation was restored, and Eybeschutz was regarded as having been vindicated. The issue was to arise again, albeit tangentially, in the 1751 dispute between Emden and Eybeschutz.