He resided at the new capital of Johor at Batu Sawar, but later moved his administration to Pasir Raja around 1609.
In 1612, at the instigation of his co-ruler and half-brother Abdullah, (better known from period historical documents as Raja Bongsu or Raja Seberang; who after 1613 ruled as Abdullah Ma'ayat Shah) and Bendahara Tun Sri Lanang oversaw the editorial and compilation process of the Malay Annals, one of the most important Malay literary works.
[1] In 1606 Alauddin allied with the Dutch to fight the Portuguese in an attempt to oust them from Malacca in a joint military campaign.
To this end he ratified two treaties with the Dutch Admiral Cornelis Matelieff de Jonge in May and September 1606.
[2] Following a crippling blockade of the Johor River in 1608 and 1609, he signed a peace agreement with the Portuguese in October 1610.