Qafih wrote extensively about the heritage of Yemenite Jews, describing in a book, “Halichot Teman”, the Jewish life in Yemen, eclipsing even the renowned works of Amram Qorah and ethnographer, Yaakov Sapir. He published several works of Yemenite Jewish provenance, such as Meor ha-Afelah by Nethanel ben Isaiah (14th-century), and Garden of the Intellects by Natan'el al-Fayyumi (12th-century). He also published a book under the title of “Shivat Tzion” Tiklal, a Yemenite prayer book reflecting the views of Maimonides in three volumes. In 1993 he published a new version under the title of “Siaḥ Yerushalayim” in four volumes (posthumously edited to six). Qafiḥ's seminal work, however, was his commentary on Maimonides' Mishne Torah, where he highlighted textual variations based on the Yemenite handwritten manuscripts of Maimonides' Code of Jewish law. Qafiḥ identified with the Dor Dai tendency, except that he did not publicly express opposition to the Zohar beyond saying that it was preferable to draw sustenance from the teachings of Maimonides. In his leadership of the Yemenite community in Israel he endeavored to maintain peace between the main factions in the community and worked to preserve Yemenite customs. In matters pertaining to Yemenite customs, even where later customs conflict with the earlier custom, Rabbi Mordechai Eliyahu regarded the opinion of Rabbi Qafiḥ, who he called Mori Yusef (Hebrew: מארי יוסף),Hebrew source: שתמיד הקפיד בלשונו לכנות את הגר"י קאפח בכינוי: "מארי", על אף שבפי אחינו הספרדים רגילים לומר "חכם" to be decisive.
