Sultan Mahmud Iskandar Shah resided at Geronggong. He had no issue and his younger brother, Raja Mansur, was given the title of Sultan Muda or Yang Di-Pertuan Muda Mansur Shah, who resided at Pulau Tiga and had five princes, Raja Radin, Raja Inu, Raja Bisnu, Raja Abdul Hamid and Raja Bongsu, of whom three would become Sultan of Perak. However, Yang Di-Pertuan Muda Mansur Shah was outlived by Sultan Mahmud Iskandar Shah (who later mangkat at the age of 120 years old).
Further tumultuous entanglements with the Dutch occurred during the reign of Sultan Mahmud Iskandar Shah. In 1653, the Dutch East Indies Company (Vereenigde Oost-Indische Compagnie) returned to Perak and renegotiated the original treaty signed by John Truijtman and Almarhum Sultan Mudzaffar Shah II (Marhum Jalilullah), vis-a-vis a piece of land in Perak for a Dutch trading outpost. The treaty also stated that Perak was to compensate for the loss of a trading outpost previously destroyed by the Malays in 1651. However, this treaty with the V.O.C. was largely ignored and most of the tin produced by Perak was smuggled out to Acheh and was traded with other lands. In 1663, V.O.C. left their Perak trading outpost but only to return two years later with naval reinforcements based at the estuary of the Sungai Perak.
In 1670, the British briefly occupied Pulau Pangkor until the V.O.C. Governor General in Batavia had instructed its forces in Melaka to take over Pulau Pangkor and build a fort at a bay in the east side of the island. Between 1676 and 1677, Dutch trading ships sailing near the coast of Perak and the Sungai Perak estuary were attacked by the Perak Malays. The Dutch fort at Pulau Pangkor was attacked by a group led by Panglima Kulub in 1690. Following the massacre, the V.O.C. finally left Perak for good.
During Sultan Mahmud Iskandar Shah’s reign, an Arab missionary named Syed Hussain Al-Faridz came to Perak to further spread to word of Islam.
In 1700, Perak was free from the Achenese sovereignty, as Acheh had been led by the reign of four consecutive Raja Perempuans for almost 60 years, weakening her power in the region. Achenese influence in Perak can still be seen today in the form of Orang Besar Lapan, and a piece of the Perak regalia named Mundam.
Sultan Mahmud reigned in Perak for 67 years and died at the age of 120 years old. He was interred at Geronggong with the title Marhum Besar Aulia Allah.