[6][7] The fate of the Johorese sultan Alauddin Riayat Shah III is disputed with some saying he was captured by the Acehnese and executed while others stated he escaped to the Lingga Island where he died in 1615.

[8] The captured Dutchmen were taken to Aceh as prisoners of war, where they apologized to Sultan, saying that they were bound by their treaty of 1606 with Johor to defend the sultan who was a friend of the Dutch, Iskandar was troubled by the fact that the Dutch had come to the defense of his Malay enemy, yet he forgave them and allowed the captives to stay in their lodge on bail of the company's goods.

[9] His younger brother, Abdullah Ma'ayat Shah known as "Raja Bongsu" was married to Iskandar Muda's sister and sent back to Johor to rule it as a Vassal of Aceh,[10][11] because of his anti-Portuguese stance, he was a better candidate, returning with 2000 Achenese to rebuild Batu Sawar.

[12] In 1614, Johor once again made a truce with the Portuguese, this political setback was a challenge to the Acehnese power equilibrium gained over Malacca, Malacca's ability to force Abdullah shows Aceh's ineffective authority over Johor,[13] and this time the Acehnese Armada of 300 and 30000 to 40000 men invaded Johor in September 1615 and for the second time destroyed Batu Sawar, Abdullah escaped and have taken refuge in Bintan Island,[14][15] In 1615, the Acehnese armada attempted to attack Portuguese Malacca, but encountered a Portuguese fleet that engaged them at the Battle of Formoso River.

[16][a][17] Having suffered thousands of casualties in the battle, the Acehnese called off the attack on Malacca and fled to Aceh.