In October 1624, R' Heller was called to the rabbinate of Nikolsburg, Moravia, and in March 1625, became rabbi of the newly reorganized community in Vienna. From 1627 until 1629, he was chief rabbi of Prague.
In 1631, he moved to the Ukraine, where he served as rabbi of Nemirov for three years. In 1634, he moved to the larger city of Ludmir (Volodymyr) in Volhynia. During his years in Volhynia and Poland, Heller was among the rabbinic leaders of the Council of Four Lands. In 1640, he worked to obtain the renewal of the synod’s decrees against simony in the rabbinate.
Finally, in 1643, he was elected head of the rabbinical court of Kraków, one of the two chief rabbis of that community. Joshua Heschel, the author of Maginne Shelomoh, was head of the yeshiva there. Four years later, Heschel died, and R' Heller succeeded him in the direction of the yeshiva as well. Heller was chief rabbi of Kraków during the Chmielnicki uprising of 1648, and until his death in 1654.
A commission was quickly appointed to inquire into R' Heller's guilt. Heller defended himself adroitly, but the commission's verdict was that R' Heller properly deserved death. Lobbying on the part of the Jewish leadership of Prague and Vienna saved him from that fate. The emperor commuted the punishment, but Heller was required to pay a very heavy fine, and his position as chief rabbi was taken away.
After spending more than a month in prison, Heller was released. He then spent two years paying off the fine. In 1631, Heller left Prague, and spent the second part of his career in the Polish-Lithuanian Commonwealth.
Several factors account for Heller's imprisonment. His arrest marked the beginning of a brief Habsburg anti-Jewish campaign, encouraged by the Papacy. Heller also had enemies within the Prague Jewish community. On account of the Thirty Years' War, the government had imposed heavy taxes on the Jewish communities of Bohemia, including that of Prague, which had to pay a yearly tax of 40,000 thalers. A commission consisting of the more prominent and wealthy members of the Jewish community was created to apportion the taxes among the people. Sadly, the members of this commission abused their positions and apportioned an undue burden of the taxes among the poor. R' Heller was associated with the wealthy leader of the Prague community at that time, Jacob Bassevi, and bore the brunt of anger against him. Meanwhile, Bassevi, who was an ally of the great general Albrecht von Wallenstein, also had enemies at the Habsburg court, and the arrest of Heller played a part in larger political machinations there.
In commemoration of his imprisonment and his release from prison, Heller established two special days of remembrance for his family and descendants. He established the 5th of Tammuz, the day on which his troubles began, as an annual fast-day, and the 1st of Adar as a day of celebration on the anniversary of his nomination to the rabbinate of Kraków. The reading of the Megillah that Heller wrote, called Megillat Eivah (Scroll of Hostility), that tells the story of his imprisonment and release, became a tradition for the descendants of Rabbi Heller. To this day, they celebrate the story of his life in a special Purim celebration.
Heller’s major halakhic work was Ma`adanei Yom Tov, a commentary to the summary of the Babylonian Talmud by Rabbi Asher ben Jehiel. Rabbi Asher’s summary was often taken by German Jews of Heller’s day to be the most authoritative statement of Jewish law, even in preference to the Shulhan Arukh. Heller’s introduction to the work endorses that view. Heller’s halakhic views, mainly on matters of ritual, are quoted by many later rabbis, especially the latyer rabbis of Prague.
Heller also authored a memoir called Megilat Eivah, as we have mentioned.
Among Heller’s many minor works are sermons and responsa. He also wrote two sets of piyyutim. The first set, from 1621, commemorates the Defenestration of Prague and the beginning of the Thirty Years War; and the escape of the Prague Jews from the sack of Prague by Habsburg troops after the Battle of White Mountain in 1620. The second set of poems, written in 1650, commemorate the Cossack massacres of 1648-1649.
Heller was a kabbalist, and even authored himself a Kabbalistic work, a commentary on Rabeinu Bahya ben Asher, based on the kabbalistic views of Moses Cordovero. But throughout most of his life, Heller was opposed to the popularization of kabbalah, and the use of kabbalistic reasoning in matters of Jewish law.
Among rabbis of his generation, Heller was exceptionally well versed in the secular sciences. His Talmudic works and his sermons show that he was interested in questions of arithemetic, astronomy, and natural science. His notes on the Giv'at ha Moreh of Joseph ben Isaac ha-Levi prove that he occupied himself with philosophy. He praised the Me'or 'Enayim of Azariah dei Rossi in spite of the anathema that his master, Judah ben Bezalel, whom he held in great esteem, had launched against the book and its author. His statement on the universal dignity of humanity is also notable, as is his openness to study of works by non-Jews. One of his sermons alludes to the “new astronomy” of Copernicus and Tycho Brahe.
Heller is also the subject of a number of folktales and legends. One well-known story about R' Heller concerns a miser who died in Kraków. R' Heller was asked where to bury him. The town leaders were disgusted by this man's lack of charity, and directed that his body be buried in a far corner of the cemetery-. A few days after the miser's death, a great cry was heard in the town, for the poor and hungry were bereft of the miser's secret generosity. The "miser" had been giving charity in the most noble fashion – secretly giving money to the local merchants, who in turn had given food, clothing and money to the poor. When this came to R' Heller's attention, he was visibly shaken. He instructed the town to bury him next to the miser upon his own death. This explains why R' Heller, one of the greatest of Talmudic scholars, is buried in such an undistinguished section of the cemetery.