His important halakhic works are: Lehem Shamayim, on the Mishnah (pt. 1, 1728; pt. 2, 1768); a letter of criticism against R. Ezekiel Katzenellenbogen, rabbi of Altona (1736); responsa, She'elat Yavez (2 pts. 1738–59), Mor u-Kezi'ah, on the Shulhan Arukh, OH, (2 pts., 1761–68). In addition, he published an important edition of the prayer book (whose parts had different names) with a valuable commentary (1745–48). This prayer book was reprinted several times. His main historical importance lies in his campaigns against the Shabbateans to which he dedicated many years. He relentlessly examined and investigated every suspicious phenomenon pertaining to the sect. He called upon the contemporary rabbis to publish excommunications and mercilessly attacked anyone suspected of supporting or showing sympathy to the Shabbateans. The Shabbateans were accustomed to introduce hints of their secret doctrine into their literary works, particularly in the field of Kabbalah. Consequently, R. Emden became an expert in uncovering such allusions and hidden meanings, and developed an extraordinarily sharp critical faculty by which he could recognize any suggestion of the Shabbatean heresy. Many books in which no one saw anything to which objection could be taken, were condemned by him as heretical. Though at times he was at fault and suspected the innocent without cause, his judgment in general was sound.

דף לב,ב-לו: דברי פולמוס מאת ר' יעקב עמדן נגד כת שבתי צבי, פסק דין שמותר למסרם למלכות, דברים על הנצרות ונגד עלילות הדם. בראשי עמודים אלה כותרות על תוכן כל עמוד ועמוד.