Torat Moshe, a commentary on the Pentateuch, was first printed in Constantinople 5354-5 (1594 CE) and has been reprinted numerous times. It is Rabbi Moshe Alshich's most popular work and it earned Rabbi Moshe a prestigious place among the great Torah commentators. Torat Moshe came to be published in the following way: It was revealed to Rabbi Caro that his student had merited one of the seventy facets of Torah exegesis. He compelled Rabbi Moshe to deliver the sermon on the following Shabbat. The sermon was received with great acclaim, and from then on, Rabbi Moshe was given the honor of delivering a sermon every week. His foremost aim in his commentary is to find fundamental moral and ethical lessons in the verses…

So popular were his sermons that people would repeat them to others, and it naturally came about that corrupted versions of his sermons were disseminated. In addition, it seems that some unscrupulous people attributed the sermons to themselves (Introduction to Torat Moshe). When Rabbi Moshe realized what had happened, he decided to commit the sermons to writing in a condensed form, which became known as Torat Moshe. It is popularly referred to, however, as "HaAlshich HaKadosh" ("The Holy Alshich").

His style in Torat Moshe is to raise a number of questions and difficulties on a verse and then answer them all together by offering a new insight into the subject matter of the verse. His foremost aim in his commentary is to find fundamental moral and ethical lessons in the verses, or point out good qualities of character, such as faith, patience, humility, and so on. The work quickly became very popular, and its author was revered as a holy man.

His other works are:

- Chavatzelet Hasharon on the Book of Daniel (Safed 5323 / 1563 CE).

- Shoshanat HaAmakim on Song of Songs (Venice (5351 / 1591 CE).

- Rav Peninim on Proverbs (Venice 5352 / 1592 CE).

- Einei Moshe on Ruth (Venice 5361 / 1601 CE).

- Devarim Nechumim on Lamentations (Venice 5361 / 1601 CE).

- Devarim Tovim on Ecclesiastes (Venice 5361 / 1601 CE).

- Masat Moshe on the Book of Esther.

- Chelkat Mechokek on Job (Venice 5363 / 1603 CE).

- Mar'ot haTzov'ot on the Early and the Later Prophets (Venice 5363-67 / 1603-7 CE).

- Romemot E-l on Psalms (Venice 5365 / 1605 CE).

A book of responsa (140 in number) is also in existence (Venice 5365 / 1605 CE). Rabbi Moshe was also a poet and one of his dirges on the exile of the Shechina, "Hikabtzu v'shim'u bnei Yaakov" ("Gather and hear, sons of Jacob") was incorporated in the midnight Tikun Chatzot prayer of several communities. She'arim, a religious philosophical work, a commentary on Bereishit Rabba, and a commentary on Talmud were all lost.