Sabon sarkin ya kafa sabon babban birni ta kogin Johor kuma, daga nan, ya ci gaba da tursasa Portuguese a arewa.Ya ci gaba da yin aiki tare da ɗan'uwansa a Perak da Sultan na Pahang don kwato Malacca, wanda a wannan lokacin ya sami kariya daga katangar A Famosa.A arewacin Sumatra a kusa da wannan lokacin, Aceh Sultanate ya fara samun tasiri mai mahimmanci akan mashigin Malacca.Da faduwar Malacca ga hannun Kirista, 'yan kasuwa musulmi sukan tsallake Malacca don goyon bayan Aceh ko kuma babban birnin Johor na Johor Lama (Kota Batu).Saboda haka, Malacca da Aceh sun zama masu fafatawa kai tsaye.Tare da Portuguese da Johor akai-akai suna kulle ƙaho, Aceh ya ƙaddamar da hare-hare da yawa a kan sassan biyu don ƙarfafa ƙarfinsa.Yunƙurin da faɗaɗawar Aceh ya ƙarfafa Portuguese da Johor don sanya hannu kan yarjejeniyar sulhu da karkatar da hankalinsu zuwa Aceh.Tsagaitawar, duk da haka, ta kasance ɗan gajeren lokaci kuma tare da Aceh ya raunana sosai, Johor da Portuguese sun sake ganin juna.A lokacin mulkin Sultan Iskandar Muda, Aceh ya kai hari Johor a shekara ta 1613 da kuma a 1615. ^[54]