The last sultan of the Malaccan dynasty, Sultan Mahmud Shah II, was known for his erratic behavior, which went largely unchecked after the death of Bendehara Habib and the subsequent appointment of Bendahara Abdul Jalil. This behavior culminated in the Sultan ordering the execution of a noble's pregnant wife for a minor infraction. In retaliation, the Sultan was killed by the aggrieved noble, leaving the throne vacant in 1699. The Orang Kayas, advisors to the sultan, turned to Sa Akar DiRaja, Raja Temenggong of Muar, who suggested that Bendahara Abdul Jalil inherit the throne. However, the succession was met with some discontent, particularly from the Orang Laut.

During this period of instability, two dominant groups in Johor—the Bugis and the Minangkabau—saw an opportunity to wield power. The Minangkabau introduced Raja Kecil, a prince claiming to be Sultan Mahmud II's posthumous son. With the promise of riches and power, the Bugis initially supported Raja Kecil. However, Raja Kecil betrayed them and crowned himself Sultan of Johor without their consent, causing the previous Sultan Abdul Jalil IV to flee and eventually be assassinated. In retaliation, the Bugis joined forces with Raja Sulaiman, the son of Sultan Abdul Jalil IV, leading to Raja Kecil's dethroning in 1722. While Raja Sulaiman ascended as Sultan, he became heavily influenced by the Bugis, who, in effect, governed Johor.

Throughout Sultan Sulaiman Badrul Alam Shah's reign in the mid-18th century, the Bugis exerted significant control over Johor's administration. Their influence grew so substantial that by 1760, various Bugis families had intermarried into the Johor royal lineage, further consolidating their dominance. Under their leadership, Johor experienced economic growth, bolstered by the integration of Chinese traders. However, by the late 18th century, Engkau Muda of the Temenggong faction began reclaiming power, laying the foundation for the sultanate's future prosperity under the guidance of Temenggong Abdul Rahman and his descendants.