Rabbi Yehonosson (Jonathan) was born in Cracow (Poland) in the year 5450 (1690). His father, Rabbi Nosson Nota, was Rabbi in Eibenschitz (Moravia), where he died, leaving Jonathan a young orphan. A wealthy Jew in Vienna took the young lad under his wing. However, the widow feared that the boy might be distracted from his Torah studies in his new surroundings. She took him back with her to Prossnitz, where she came to live. There, Jonathan studied Torah in the Yeshiva of the Gaon Rabbi Meir Eisenstadt, author of Panim Meiroth. Soon also his mother died, and Jonathan found a foster-home with Rabbi Yitzchak Schapiro, chief rabbi of Prague and Bohemia. When he became of marriageable age, Rabbi Jonathan married the chief rabbi's daughter.
For several years, Rabbi Jonathan lived in his father-in-law's house and concentrated on his studies quietly and peacefully. He became known as a brilliant Talmudic scholar. He was only eighteen years old when he was invited to become rabbi of Jungbunzlau, Czechoslovakia. Three years later he returned to Prague to head the famous Yeshiva there. He also excelled as a very impressive and inspiring preacher. After spending a year in concentrated study at the home of his wife's grandfather, a prominent and learned man in Hamburg named Mordechai, he once again returned to Prague (in 5472). Now he established his own Yeshiva and attracted many young scholars, for his reputation as a Talmudic authority and excellent teacher had spread far and wide.
Rabbi Jonathan's keen intellect sought knowledge in other fields as well, particularly in the inner mystical wisdom of the Torah, the Kabbala.
Rabbi Jonathan's fame as a preacher and teacher rose to new heights. He was greatly esteemed also by prominent non-Jewish scholars, among them the Jesuit bishop Hasselbauer. Rabbi Jonathan Eybeschutz used his good influence to obtain permission from the bishop to print the Talmud which had been forbidden by the Church who charged that the Talmud had anti-Christian references. It was necessary, however, to omit any passage to which the censors might object. Rabbi Jonathan's high reputation also stood him in good stead when he traveled to Vienna to intervene on behalf of his brethren in Prague and Bohemia. In 1741, he was elected rabbi of Metz. That was the time when war broke out between Prussia and Austria, and the French army, in support of Prussia, invaded Bohemia. Rabbi Jonathan found favor with the French and he received safe conduct to Metz. In 5502 (1742), Rabbi Jonathan Eybeschutz left Prague with all his family to take up his post in Metz. Most of their possessions were left behind. Later, when the French withdrew from Prague and Bohemia and the Austrian government reestablished its reign there, the government considered Rabbi Eybeschutz's cooperation with the French as a treacherous act. He was not permitted ever to return to Prague, and all his property left behind was confiscated.
Rabbi Jonathan Eybescbutz was greatly esteemed in Metz and he could have led a peaceful and productive life there. But the trouble that befell his brethren in Bohemia and Moravia made him very unhappy. In 1745 the war between Prussia and Austro-Hungary broke out again, and the Austro-Hungarian troops who had overrun these provinces considered the Jews fair game to rob and pillage. To add to the Jews' misery, the Austrian government ordered the expulsion of the Jews from the said provinces.
At this time Rabbi Jonathan Eybeschutz tried all he could to ease the plight of his brethren. He enlisted the aid of the Jewish leaders in Rome to plead with the Pope to use his power in behalf of the persecuted, defenseless Jews. He appealed to the Empress of Austria to rescind the expulsion order, and he turned to various Jewish communities in the south of France and elsewhere to raise funds for the hungry and needy.
Rabbi Jonathan held his post in Metz for nine years. During this time, many promising young scholars came to his Yeshiva in Metz to study the Talmud. In the month of Elul, 5510 (1750) Rabbi Jonathan's friends in Altona and Hamburg appointed him as chief rabbi of the three united communities AHU (Altona, Hamburg and Wansbeck).
In the very first year of Rabbi Jonathan's taking up his position, there was a sudden rise in the number of deaths in childbirth. Having the reputation of a saintly kabbalist and miracle worker, many Jews turned to their rabbi for help. One of the ways to counteract the danger, which had often been practiced among cabalists and miracle men, was to write special amulets (kameoth), and Rabbi Jonathan wrote a number of them to be worn by expectant mothers, as he used to do also in Metz. An amulet which was supposed to have been written by Rabbi Jonathan was brought to the attention of Rabbi Jacob Emden, an outstanding Talmudist and kabbalist in Altona. The latter deciphered the mystical writing and found in it a hidden invocation to Shabbatai Tzevi. Rabbi Emden accused Rabbi Eybeschutz of being a follower of Shabbatai Tzevi. The leaders of the community rushed to the defense of their rabbi. They proclaimed a boycott of Rabbi Emden's synagogue and ordered Rabbi Emden to leave town within six months. In the meantime the controversy spread to other cities in Germany and Poland, as some of the most celebrated rabbis took part in support of one or the other of the two sides in the controversy. Rabbi Emden saw himself compelled to leave Altona, and he secretly went to his brother-in-law Rabbi Arye-Leib, rabbi of the Ashkenazic community in Amsterdam. From there be continued his fight, writing to the Council of Rabbis of the Four Lands meeting in Constantine, and pressed his charges.
Finally Rabbi Jonathan Eybeschutz decided to bring his case before the Council of the Four Lands which convened in Jaroslav for this purpose in 1753. Rabbi Jonathan's innocence was then established, and the dispute which had caused much disunity and disrespect in many a Jewish community and which had involved also the king of Denmark came to an end. Rabbi Jonathan Eybeschutz was again confirmed in his office by the Hamburg Senate in the month of Kislev, 5517 (1757), and he was not troubled any more.
Rabbi Jonathan Eybeschutz spent the rest of his life peacefully, concentrating on his books, which represent an outstanding contribution to Rabbinic literature.
His main works on Halacha are his Urim Vetumim, a commentary on Shulchan Aruch, Choshen Mishpat, and Keretbi Ufelethi, on Yore De'ah. Other works such as Binah Ittim, dealt with other sections and subjects of Halacha. Very highly regarded and popular are his works in drush (homiletics), especially his Yaaroth Devash, in two volumes, and Tifereth Yehonathan. Most of his works were published and reprinted many times. He also wrote several works on Kabbala, of which one, Shem Olam, was published (Vienna, 1891). In connection with the dispute with Rabbi Emden, Rabbi Jonathan wrote a special volume of defense, Luchoth Habrith (Tablets of Testimony), in which he describes the whole dispute and refutes the charges against him. It includes also the letters of recommendation which he had received from leading rabbis who came to his defense. It is a masterpiece of restrained and wise writing, which proves that he had been a victim of an overzealous, though well-meaning, defender of Judaism.