Like his father, Sultan Ali was a puppet monarch and played a minimal role in the administrative affairs of the state, which came under the charge of the Temenggong and the British.

[8] A proclamation by the British colonial government in September 1840 granted him the right as the legitimate heir as his father's successor, but not amounting to recognition as the "Sultan of Johor".

[10] However, unlike the Temenggong, Sultan Ali was unwilling to involve himself with the affairs of the state but at the same time complained about receiving an insufficient allowance from the British.

[13] As a result of economic and political pressure from these traders, the Governor did consider granting formal recognition to Sultan Ali as the legitimate ruler of Johor, but in the process, he received a strong protest from Temenggong Daeng Ibrahim and his young son, Abu Bakar.

On the other hand, Sultan Ali had expressed his wish to the governor that the Kesang territory (around Muar) should be directly governed by him, citing reasons that some of his ancestors were buried there.

[19] A treaty was concluded on 10 March 1855, in which Sultan Ali formally ceded his sovereignty rights of Johor to the Temenggong permanently with the exception of the Kesang territory (around Muar).

[23] His relations with Temenggong Daeng Ibrahim remained strained; in 1860, Sultan Ali allowed a Bugis adventurer, Suliwatang, the chiefs of Rembau and Sungei Ujong to settle in Muar and prepare themselves for an attack on Johor.

Eleven years later in 1873, attempts made by Suliwatang to collect custom taxes from inhabitants at the Muar estuary led to further conflict with Abu Bakar's (who became Maharaja in 1868) men.

[1] Sultan Ali spent his last years in Umbai, Malacca, and supported himself with a small monthly stipend which the British East India Company had granted him.

[26] He built a palace for himself and lived with his third wife, Cik' Sembuk until his death in June 1877, and was buried in a Mausoleum within the confines of the Umbai mosque.

His decision was met with considerable disproval among the some Malays in Singapore, who felt that Tengku Alam Shah should be the heir to the Kesang territory as he was the oldest son with Daeng Siti, who was the daughter of a Bugis nobleman, while Cik' Sembuk was a commoner.

The British Governor handed over administrative charge of the Kesang territory over to the Maharaja, which upset Tengku Alam Shah and many of his supporters.