Shaykh Muhammad ibn Al-Habib Al-Amghari was born in Fez in 1290 AH / 1871. His family hailed from Marrakesh, and his father, Sidi Al-Habib, a righteous person, migrated to Fez. Shaykh Muhammad was raised with good character and high principles, and received full care and love from his parents, as he was an only child (may Allah be pleased with him). When he reached the age of discernment, his father sent him to the Quranic school in Qantarah Abur Roos in the Sharabliyin area in 1295 AH / 1876. He memorized the Noble Quran in a short period of time under the guidance of the jurists Sidi Ibn Al-Hashimi Al-Sanhaji and Sidi Ahmad Al-Filali in the Qasbah An-Nawwar school. During this time, someone with great spiritual states visited and looked at the students with the eye of inner sight, predicting that Shaykh Muhammad ibn Al-Habib would become a scrupulous scholar, shaykh and spiritual nurturer.

He took knowledge from the great scholar and jurist, Sidi Muhammad Al-Irari, the Ajrumiyyah, As-Sullam by Al-Bannani, and a section of the Shama'il Muhammadiyah of At-Tirmidhi. In 1300 AH/1881, at the age of 29, he joined the Qarawiyin mosque and studied under many scholars. His excellence, perfect etiquette and steadfastness endeared him to all his teachers. May Allah be pleased with him. In 1312 AH / 1891, when he completed his studies at Al-Qarawiyin, he was granted permission (ijazah) by all his teachers in all the sciences and arts he had learned from them. He then began teaching at the Qasbah An-Nawwar mosque and the Qarawiyin mosque, imparting all the knowledge he learned from his teachers.

One of Shaykh Ibn Al-Habib's distinguished qualities was his humility and respect for people's circumstances and stations in life, as well as his eagerness to communicate with scholars and shaykhs regardless of their affiliation to a particular school of thought. Shaykh Muhammad ibn Al-Habib had a bright aura since his childhood and was accepted and beloved by all who met him or heard about him. This was a gift from Allah that He bestows upon His righteous servants, endearing them to people's hearts and causing their tongues to praise them, and granting them acceptance on earth. This was evidenced by the fact that many saints and righteous people who knew his precious nature admired him. Shaykh Muhammad ibn Al-Habib narrated an incident that happened during his Quran memorization period. His teacher, the righteous jurist Sidi Ahmad Al-Filali, who was one of the friends of Allah the Exalted, pointed to the students, looking at them with the eye of inner sight, and said: "This one will be a butcher, and this one will be a tailor, and so on," until he pointed to our Shaykh and said: "This one will become a perfect and scrupulous scholar who remembers Allah." Shaykh Muhammad ibn Al-Habib passed away on his way to Hajj with his disciples in the city of Blida, Algeria, on 23 Dhul Qa'dah 1391 AH, and was buried in his zawiyah in Meknes.