Hacham Zion Cohen Yehonatan was born in Djerba in 1872, the only son of Maryuma and Hacham Shushan Cohen Yehonatan. In 1897, at the age of 25, he was appointed dayan on the island of Djerba. In 1912, at the age of 40, he was appointed President of the Djerba rabbinic courts and remained in this role until his death.
Hacham Zion Cohen Yehonatan had seven sons and two daughters; his eldest son is Rabbi David Hacohen Yehonatan and the youngest son is Rabbi Yoseph Hacohen Yehonatan.
In 1919 he was party to the founding of the Attereth Zion organization that dealt in Jewish and Zionist education, promoting the Hebrew language, and raising funds to support the Jewish settlement in the Land of Israel and to redeem land.
Hacham Zion Cohen Yehonatan was renowned for his Torah learning and deep knowledge of Talmud and halakha. He was said to have completed in-depth study of the entire Talmud three times during his lifetime. The sage gave public Torah classes that were held in his home and at his uncle Hacham Sassi Maatuq's yeshiva. His classes were known as the Four Cubits of Halakha.
One of his close students was Hacham Moshe Khalfon Hacohen, who presided alongside him in the rabbinic court. Hacham Zion Cohen Yehonatan once went to the community committee requesting that his salary be increased. This raised quite a tumult, for his family was considered wealthy. He insisted, nevertheless. It eventually became clear that the sage, knowing the distress of his student, had asked for a salary increase knowing that his student, who presided alongside him, would thus also receive a salary increase. After his demise, his daughter recounted how her father would send her out every week with a cloth bag of coins containing his weekly salary to distribute to the city's poor and needy people.
Hacham Zion Cohen Yehonatan passed away after an illness on 26 Av, 5691 (1931) and was buried on the island of Djerba. His remains were brought to Israel in 2010 and buried in Moshav Berachia.
After his death, several of his books were published by his sons and students: Zion B'Mishpat Tipadeh in three volumes – original commentary on the weekly Torah Reading portions, Ethics of Our Fathers and the Passover Haggadah; Sha'arei Ratzon – original commentary on the Talmud; Shivat Zion –responsa on Orach Haim.