In 1624, he was appointed Chief Rabbi of Vienna. Earlier he had served for twenty-eight years as a dayan, a judge in matters of Jewish Law, in Prague, and for a short time as the Rabbi of Nikolsburg in Moravia. He was chosen to be Chief Rabbi of Prague in 1627, following in the tradition of his great teachers, the Maharal and the Kli Yakar.
As a result of the costs of the Thirty Years War, the Jews of Prague were assessed a huge tax of forty thousand thalers (it is likely that the thaler was an antecedent of the American dollar). The rabbi, in an effort to be fair, assessed the rich citizens of Prague considerably more than their less affluent neighbors, which did not please the wealthier and more influential group. The richest among them, along with several co-horts and members of the government and the Church, agreed on a plan to frame the Rabbi.
It was falsely alleged that Rabbi Heller had defamed Christianity in his works Maadanei Melech and Lechem Chamudos. A mock trial was held, in which the Rabbi more than held his own, so that the death sentence that was the usual penalty for such crimes was commuted to a prison sentence for the Rabbi and expulsion for the Jewish Community, except for the Chief Accuser who, as mentioned above, was himself Jewish. Through the efforts of various diplomatic channels set into motion by his son, Rabbi Heller was released from prison and the edict of expulsion against the community was rescinded. For all of his future descendants, the Tosafos Yom Tov decreed a fast day on the anniversary of his imprisonment. In Megilas Eivah (The Megila of Hatred), a parallel name to Megilas Eichah, that describes the tragedy that befell Yerushalayim, Rabbi Yom Tov Lippmann Heller describes his own bitter experience.
After a confinement of forty days, Rabbi Heller was released from prison. On Rosh Chodesh Iyar, Rabbi Yom Tov was offered the position of Rabbi in the town of Ludmir. After accepting that position, he turned his attention to another problem. Unworthy candidates were purchasing rabbinical positions from local princes. There was a standing ban against this practice but the ban was breaking down. The Rav became an active participant in a rabbinical convention known as the Vaad Arba HaAratzos, The Council of the Four Lands, and the ban was renewed and intensified. This active involvement threatened to place Rabbi Yom Tov in jeopardy again. But this time his fortune changed for the better.
In 1643, he was offered the position of Rabbi of Krakow, succeeding Rabbi Yoel Sirkus (the Bach). He also joined the author of the Pnei Yehoshua as co-Rosh Yeshivah of the Yeshiva of Krakow, a position that was among the highest in the Jewish world at that time. The Tosafos Yom Tov decreed upon his descendants that they celebrate the anniversary of his election to the Rabbinate of Krakow as a holiday.
The Chmielnicki Massacres of Tach VTat (1648-1649) produced many agunos, women whose husbands were missing with none to testify as to the actual death. Rabbi Heller did all that he could to find ways that they could re-marry.
As mentioned at the beginning, the most famous of his writings was a commentary on all of the Mishnah, in which he incorporated his vast knowledge of the Talmud to clarify the meaning of the more concise Mishnah. This commentary is called Tosafos Yom Tov, after his name, with the incorporation of Tosafos, because he viewed the role of his commentary to the Mishnah as analogous to the role of the Baalei HaTosafos in relation to Rashi and the Talmud.
A few of the other sefarim that he wrote were Tzuras HaBayis, a description of the Third Temple as found in the Book of Yechezkel, and a two-part commentary on the works of the Rosh, Maadanei Melech and Lechem Chamudos, innocent enough in design but serious enough when their contents were distorted, to nearly cost him his life and expulsion for the entire Jewish community.
The Tosafos Yom Tov was niftar in Krakow in 1654. Among his many outstanding descendants was Rabbi Aryeh Leib HaKohen, the Ketzos HaChoshen.
Sources: Orthodox Union