Sarkin Musulmi na karshe na daular Malacca, Sultan Mahmud Shah II, ya yi suna da halin rashin gaskiya, wanda ba a kula da shi ba bayan rasuwar Bendehara Habib da kuma nadin Bendahara Abdul Jalil.Wannan dabi'a ta kai har Sarkin Musulmi ya ba da umarnin a kashe matar wani mutum mai ciki saboda karamin laifi.A cikin ramuwar gayya, an kashe Sarkin da aka yi wa mai martaba, inda ya bar gadon sarauta a sarari a cikin 1699. Orang Kayas, mashawartan sarkin, ya juya zuwa Sa Akar DiRaja, Raja Temenggong na Muar, wanda ya ba da shawarar cewa Bendahara Abdul Jalil ya gaji sarauta.Koyaya, magajin ya gamu da wasu rashin gamsuwa, musamman daga Orang Laut.A cikin wannan lokaci na rashin zaman lafiya, ƙungiyoyi biyu masu rinjaye a Johor - Bugis da Minangkabau - sun ga damar yin amfani da mulki.Minangkabau ya gabatar da Raja Kecil, wani basarake da ke iƙirarin cewa shi ɗan Sultan Mahmud na biyu ne bayan mutuwarsa.Tare da alƙawarin wadata da iko, Bugis ya fara tallafawa Raja Kecil.Sai dai Raja Kecil ya ci amanar su, ya nada kansa Sarkin Johor ba tare da amincewar su ba, wanda hakan ya sa tsohon Sarkin Musulmi Abdul Jalil IV ya gudu daga karshe aka kashe shi.A matsayin ramuwar gayya, sai Bugis suka haɗu tare da Raja Sulaiman ɗan Sultan Abdul Jalil IV, wanda ya kai ga tsige Raja Kecil a 1722. Yayin da Raja Sulaiman ya hau Sarkin Musulmi, Bugis ya rinjaye shi, wanda, a zahiri, yana mulkin Johor.A tsawon lokacin mulkin Sultan Sulaiman Badrul Alam Shah a tsakiyar karni na 18, Bugis ya ba da iko sosai kan gwamnatin Johor.Tasirinsu ya karu sosai har zuwa 1760, iyalai daban-daban na Bugis sun yi aure cikin zuriyar sarautar Johor, suna ƙara ƙarfafa ikonsu.A karkashin jagorancinsu, Johor ya sami bunkasuwar tattalin arziki, da hadin gwiwar 'yan kasuwa na kasar Sin.Sai dai kuma, a karshen karni na 18, Engkau Muda na bangaren Temenggong ya fara kwato madafun iko, inda ya kafa harsashin samar da ci gaban masarautar a nan gaba karkashin jagorancin Temenggong Abdul Rahman da zuriyarsa.