As one of the leading rabbinic authorities of his day, Kluger issued rulings on many complex halachic questions. One of his most notable decisions was that not only did machine made matzo not meet the halachic requirements necessary to properly fulfill the requirement of eating matzo on Pesach, but that it very possibly had the status of leavened bread, consumption of which is strictly prohibited on Pesach. Rabbi Yosef Shaul Nathansonpublished a strongly worded rebuttal to the points Kluger had raised, and argued that on the contrary, machine made matzo was superior in all respects to the hand made version. The issue evolved into a significant controversy, many points of which are still debated today. Kluger, in the course of his research into the subject, came to the conclusion that he had received a somewhat inaccurate description of the technical operational details of the machines, and modified his position accordingly. Kluger was well known for his fierce opposition to the haskalah movement, and his firm adherence to tradition. In his responsa, Kluger discusses an incident where a group gathered to study the controversial works of Moses Mendelssohn. A quarrel erupted, and Mendelssohn's books were seized and burnt. Kluger wrote that while the burning of the books was probably not the appropriate course of action, they were certainly correct to be enraged and to protest the study of Mendelssohn's work. Kluger explained that he saw fit to condemn Mendelssohn and his works for several reasons. Among his arguments, he wrote
...and furthermore, go out and see what his students, and all those who study his books, are - they are all complete evildoers... And his books are not studied except by the most worthless people, who violate the whole Torah... And every person who fears heaven flees from him like from a snake or scorpion.
Works
During his long life Rabbi Kluger wrote a great number of works—one hundred and sixty volumes. He wrote on all the branches of rabbinical literature as well as on Biblical and Talmudic exegesis. Many of these writings remain in manuscript form. Among his published works are:
Sefer Ha-Chayim, novellæ on Shulchan Aruch, Orach Chayim
Mei Niddah, halachic and haggadic novellæ on Gemara Niddah
Rabbi Kluger's takkanos concerning slaughtering are printed in Rabbi Ganzfried's Toras Zevach, and two of his responsa in Rabbi David Solomon Eybeschütz's Ne'os Deshe.