Of his books the following should be especially noted: Magen Avot: Commentary on Avot de–Rabbi Natan (in the Oxford Bodleian Ms.); Lekah Tov: Commentary on the Scroll of Esther (Safed, 1577). This was the first book published in Safed; it was published for a second time in a photocopied edition (Jerusalem, 1976). This work contains a long commentary on the sages’ sermons on the Scroll of Esther, constituting both a literal and homiletic interpretation; Novellae on tractate Bava Kamma. Chapters 5–6 were printed at the end of his responsa (Venice, 1964); A total of 296 of his responsa were printed by Rabbi Yom Tov ben Akiva Zahalon in the Venice edition; another 240 responsa can be found in the Oxford Ms. and were published by the Jerusalem Institute (Jerusalem, 1980–81) in two volumes. The responsa deal mostly with subjects pertaining to Hilkhot Even ha–Ezer and Hoshen Mishpat in the Shulhan Arukh. Yom Tov Zahalon’s responsa were accepted as law. They contain historical information and details of customs and reforms in Safed and the Ashkenazi and Sephardi communities in Jerusalem, particularly the inferior position of the latter in comparison with the Ashkenzi community when it came to the distribution of charitable donations. Zahalon reveals himself as forceful, uncompromising and sometimes sharp–tongued, though he tends to accept the opinions of earlier sages. He often disagrees with the rulings of R. Joseph Caro in the Shulhan Arukh but also explains at times the language and reasoning of the Shulhan Arukh.
כה דף: חידושי (פרק) איזהו נשך; פרק השוכר את האומנין. דף כה,ב: דברים מאת המגיה, ר' משה ב"ר דניאל מאגורו.  דף בסוף: "הקדמה למפתחות הספר" והמפתחות, מאת ר' שלמה ב"ר ישעיה ניצה (תולעת שנ"י). בדברי-סיום שהוסיף, הוא כותב: "לייפות ולהדר שער הספר בצורה נאותה כמשפט הדפוס ציירו התלמידים... צורח המשכן ובית השלישי", שנדפסו בשער ומעבר לשער. ברוב הטפסים נשמטו  דף בסוף.