Yehuda wrote many books. He was the author of Mayim Amukkim(deep waters), a commentary on the torah and haftorahs (which was later commented on by Petahiah Mordecai BERDUGOamong others although unpublished until 1910). The book was republished in 1975, by one of his descendants also named Yehuda BERDUGO, along with commentaries from Rabbi Hay Yaacov Zrihen of Tiberius who in the introduction describes Yehuda mim 'mokim as the Maimonides of Morocco. This book was supposed to be published along with Rabbi Hayim Benattar's Or Hayim. However, Rabbi Benattar had to leave Morocco suddenly before he could take the manuscript. Many commentaries have been written on Mayim Amukkim despite its late publication (See for example those of Rabbi Lasri of Algers, Moshe ELBAZ of Sefrou, or Yaakov and Yossef BERDUGO of Meknes.) Until its publication the book (like other classic works by the Mashbir) were copied by hand.
Some of Yehuda mim 'mokim BERDUGO's responsa have been published in the responsa of Jacob ibn Zur. Other responsa and Mahane Yeouda have not yet been published.
He had two sons.