Kota Batu was sacked and burnt by the Acehnese in 1564, and Alauddin was taken to Aceh and killed.

[1] In the early 1570s, the sultan Ali Jalla returned to the Kota Batu area and reestablished the capital at Johor Lama.

Ali Jalla then forced ships to go Johor Lama, and attacked Melaka in January 1587.

The fortified city was defended by 12,000 men, but the Portuguese prevailed and destroyed the fort.

For some time it continued to be used as a port for larger ships where goods could then be moved upstream to towns such as Batu Sawar.