The new sultan established a new capital by the Johor River and, from there, continued to harass the Portuguese in the north. He consistently worked together with his brother in Perak and the Sultan of Pahang to retake Malacca, which by this time was protected by the fort A Famosa.

On the northern part of Sumatra around the same period, Aceh Sultanate was beginning to gain substantial influence over the Straits of Malacca. With the fall of Malacca to Christian hands, Muslim traders often skipped Malacca in favour of Aceh or also of Johor's capital Johor Lama (Kota Batu). Therefore, Malacca and Aceh became direct competitors.

With the Portuguese and Johor frequently locking horns, Aceh launched multiple raids against both sides to tighten its grip over the straits. The rise and expansion of Aceh encouraged the Portuguese and Johor to sign a truce and divert their attention to Aceh. The truce, however, was short-lived and with Aceh severely weakened, Johor and the Portuguese had each other in their sights again. During the rule of Sultan Iskandar Muda, Aceh attacked Johor in 1613 and again in 1615.^[54]