Hacham Khalifa Ben Malka was born in Safi, Morocco. An only child, he lost both his parents at a young age. He learned Torah first from Hacham Joseph Bueno de Mesquita in the city of his birth and then wandered from city to city until he reached Fes, where he studied in Hacham Yehuda Ben Attar and Hacham Samuel Hatzarfati's yeshiva.
In his book, he writes, in rhyme: "I have been alone from the day of my birth to this day. I am impoverished and alone, for my father and mother have left me. I have neither uncles nor brothers, my lot and salvation come from God, and the Father of orphans has led me to the great charity and benevolence of teachers and rabbis throughout the cities of the Maghreb."
He returned to Safi to study in Hacham Joseph Bueno de Mesquita's yeshiva. Hacham Joseph Bueno de Mesquita raised him like his own son, sharing his wisdom, books and all his possessions with him.
When he reached adulthood and achieved independence, he moved to the city of Agadir. With the help of Hacham Shlomo Ben Yeshurun, his teacher's nephew, he began to deal in commerce. His efforts met with success and his business flourished. He and his friend Hacham Yaakov Gedalia transformed their synagogue into a spiritual center and study house, where Hacham Khalifa Ben Malka preached Torah to the public and maintained his Torah study on a regular basis.
Hacham Khalifa Ben Malka married and had children, but his firstborn son, David, died at age eleven.
Hacham Khalifa Ben Malka passed away at a ripe old age on 3 Elul, 5520 (1760). He authored three works: Kaph Naqui – on the siddur prayer book and containing a collection of aphorisms, Rach VaTov and Kol Rina.