The young Alimuddin initially attended the school of his father, Badar ud-Din I, and was later sent to Batavia, Dutch East Indies, to complete his education.
On 12 July 1744, Philip V of Spain sent him a letter requesting permission for missionaries from the Society of Jesus to propagate Christianity in the southern Philippines.
A party was formed under the leadership of the Sultan's brother, Prince Bantilan, for the purpose of expelling the missionaries and deposing Azim ud-Din I. Hostilities increased and civil war became imminent.
Overpowered, disheartened, and grieved, Azim ud-Din I fled Jolo with his family and retinue for Zamboanga, where he sought the aid of Spain against Bantilan's unopposed seizure of power.
In Manila, Governor-General Juan de Arechederra, Bishop of Nueva Segovia, gave him a reception befitting a prince of high rank.
The following year, he was restored to the throne by the British,[3] upon whose departure from Manila after the signing of the Treaty of Paris saw raids by Sulu pirates on the city intensify.
He had a reputation amongst his subjects as "an authority almost supreme," earning him the title "Chief of Pandita" for his erudite and precise explanations of the Qur'an.