According to the testimony of R. Joseph Ergas, in Leghorn, Hayon disclosed to him his belief in Shabbetai Zevi. In 1711, in Venice, he published his small book Raza de-Yihuda on the meaning of the verse on the unity of G-d, Shema Yisrael, as an abridgment of his larger work to which he added, in the meantime, a second commentary. The rabbis of Venice gave approbations to this booklet without understanding its intent. The book did not arouse controversy. Later, Hayon moved to Prague where he was received with great honor in scholarly circles and gained approval for Oz le-Elohim, his main work, and Divrei Nehemyah, a book of sermons. David Oppenheim approbated Divrei Nehemyah and Hayon altered the approbation to include the kabbalistic Oz le-Elohim as well. R. Naphtali Cohen, who at first befriended Hayon, kept him at a distance after a rumor got about that connected him with the Doenmeh in Salonika. Hayon traveled via Moravia and Silesia to Berlin where, in 1713, supported by the wealthy members of the community, he succeeded in publishing Oz le-Elohim. It was daring of Hayon to publish a text which in many manuscripts was circulated then as a work of Shabbetai Zevi. With great acumen, he tried to prove in his two commentaries that this doctrine was firmly based in the classical texts of the Kabbalah.

In June 1713 Hayon left Berlin for Amsterdam. Apparently he knew of the hidden Shabbatean tendency of R. Solomon Ayllon, rabbi of the Sephardi congregation. Indeed, Hayon received the patronage of Ayllon, his bet din, and the parnasim of the community. However, a bitter and complex struggle developed between the supporters of Hayon and those of R. Zevi Ashkenazi, the rabbi of the Ashkenazi community, and of R. Moses Hagiz who knew of Hayon's early quarrels in Erez Israel and recognized the Shabbatean "heresy" in his opinions, when they investigated his book. In this controversy, relevant factors (the true views of Hayon and his Shabbateanism) and personal factors (the arrogant behavior of R. Zevi Ashkenazi, personal antagonisms) are mingled. Essentially, the accusers of Hayon were right but from a formal and procedural point of view the Sephardi bet din was right. The quarrel aroused strong emotions, at first in Amsterdam, in the summer and the winter of 1713, and it swiftly spread to other countries. R. Naphtali Cohen apologized for his previous approval of Hayon and excommunicated him. So did Italian rabbis to whom both sides turned to for support. The leaders were R. Judah Brieli of Mantua and R. Samson Morpurgo of Ancona. Most of the participants in the controversy had not actually seen the books of Hayon and depended only on the letters from both sides.

R. Zevi Ashkenazi and R. Moses Hagiz were forced to leave Amsterdam. However, the intervention of the rabbis of Smyrna and Constantinople, who excommunicated Hayon and condemned his works in 1714, decided the struggle against Hayon, whose supporters advised him to return to Turkey in order to obtain the annulment of the excommunication. Hayon returned and attempted to achieve this but he succeeded only partially. In his old age, he went back to Europe where in the pamphlet Ha-Kolot Yehdalun (1725) he published some documents in his favor. His journey was unsuccessful because R. Moses Hagiz again came out against him in the booklet Lehishat Saraf (Hanau, 1726) where he threw suspicion on several of the documents, or on the circumstances under which they were signed. Most of the communities did not allow him access and even Ayllon refused to receive him in Amsterdam. Hayon wandered to North Africa and apparently died there before 1730. According to Hagiz, his son converted to Catholicism in order to take revenge on his father's persecutors and was active in Italy.

התיבה "אמשטרדם" מובלטת באותיות גדולות. חידושים על התורה בדרך הדרש והקבלה. עיין: ג' שלום, האנציקלופדיה העברית, כרך יז, תשכ"ה, עמ' 350: "ספר דברי נחמיה ובו דרשה ארוכה, שאותה ניתן לפרש הן כסניגוריה בעקיפין על כת השבתאים המומרים בסאלוניקי והן כביקורת עליהם".

הסכמות: ר' דוד ב"ר אברהם אופנהיים, פראג, ב אדר-ב תע"ב; ר' גבריאל ב"ר יהודא ליב [עשקעלעס] מקראקא, נ"ש [ניקלשבורג], כב סיון תע"ב; ר' אהרן [ב"ר יצחק בנימין וואלף], ברלין, כו טבת תע"ג; ר' יהודא ליב ב"ר משה, גלוגא, ערב ראש-חודש אלול תע"ב.