Rabbi Yehuda ben Atar was born in Fez, Morocco, in the month of Elul 5415 (1655). His name, "Attar", means "perfumer" in Arabic, after his ancestors' trade. His father, Rabbi Yaakov, died at twenty-three; young Yehuda had to work for a living and became a skilled goldsmith. All his life, even as a rabbi, he lived from the work of his hands and refused any salary from public funds. Moroccan Jews call him "Rabbi Yehuda HaKadosh".

A student of Rabbi Vidal HaTzarfati III and Rabbi Menachem Serero, he was appointed a dayan in Fez alongside them in 1698, at forty-three. In 1701 he had to move to Meknes with many Jews of Fez, persecuted and crushed by taxes under Sultan Moulay Ismail; he sat on the rabbinical court there and from 1713 was its sole dayan. Back in Fez, he led the community and headed the rabbinical court for many years.

He wrote Minchat Yehuda, as well as rulings and ordinances (takanot), signed with the great sages of his generation, which guided Moroccan communal life. Tradition tells of many miracles about him, notably that he was thrown into a lions' den on the sultan's orders and emerged unharmed.

He passed away on 19 Sivan 5493 (1733) and rests in the Jewish cemetery of Fez, where his tomb remains a place of pilgrimage.