The Dutch-Johor agreement gave the Dutch control of the city, with Johor recovering the surrounding territory. Trasure and other booty captured from the Portuguese defenders were also to be distributed equally between the Dutch and the Johor Malays. Dutch ships were also to be exempt from taxes and duties in all Johor ports and Johor was expected to wage war on any Portuguese and Spaniard shipping. In return, Johor was to be give all the artillery captured at Melaka and the Johor Sultan was even allowed to live in Melaka, at Kampong Kling, under the protection of the Dutch government. In addition, the Dutch promised not to interfere with Malay religion and customs in the territories under their control.

In April 1606, the Dutch launched their first assault on Melaka with a force of 700 soldiers. Bandar Hilir and Tranquerah were torched and over 18,000 cannon balls rained on the town and fortress. Six thousand people died from the bombardment, hunger and disease in the three-month siege but the defenders held - supported by a force of Japanese mercenaries under the command of Furtado de Mendoca. The Dutch were finally beaten back by Portuguese reinforcements from Goa and Matelief was forced to withdraw to Johor to regroup his forces.

In 1608, another fleet under Pieter Willemszoon Verhoef, consisting of 13 ships, blockaded Melaka and raidied Portuguese shipping along the length of the Straits. Soldiers were also landed on a small island near the port, Pulau Pinang, and a garrison was set up. However, no help was forthcoming from the Johor Sultan and Verhoef was forced to withdraw to the Johor capital of Batu Sawar. There, he supplied the Johor Malays with money, cannon, bullets and twenty barrels of gunpowder to fight the Portuguese.

For the next three decades, the Dutch were preoccupied with the conquests in Java and it was not until June 1636 when a combined Dutch and Johor fleet bombarded the harbour and destroyed over 20 Portuguese ships. Another Dutch force was amassed against Melaka in June 1640 and landed on the outskirts of the city. A force of twleve ships and six boats deployed around Melaka harbour in a crescent formation and proceeded to bombard the port and fortress. In the meantime, troops landed ashore and constructed earthwork artillery fortifications from which they bombarded the city. The Johor Malays assisted the besieging force by patrolling the Straits and stopping any shipments of food or supplies bound for Melaka. Johor forces also raided the surrounding countryside, torching any padi fields and farms that might be able to provide food to the besieged city.

Engraving on a Dutch tombstone, Melaka

As the months wore on, it was later evident that this assistance was essential. Artillery bombardments on the stout walls of 'A Famosa' were ineffective and assaults by Dutch troops on the ramparts were thrown back each time with heavy casualties - the only way for Melaka to fall was to starve the city to death. In the following months, starvation and disease gripped the stricken inhabitants of Melaka. Out of a population of 20,000 people, it was estimated that more than 7,000 people had already died in the city, many thousands more had fled and there remained only 3000 in the fortress. Those who remained were reduced to eating dogs and cats. A starving mother was also reported to have devoured her dead child. The Dutch intensified their land attacks, this time bolstered by a fleet of forty ships from the Johor Sultan and 1500 Johor Malays and Minangkabaus from Naning and Rembau.

In August, the combined force stormed the first line of Portuguese fortifications at Tranquera and drove hundreds of its Portuguese defenders into 'A Famosa'. From their newly-won bridgehead at Tranquerah, the Dutch-Malay forces were now within pistol range of the fortress and they could let loose a deadly shower of bullets and cannon balls on the sick and starving defenders.

On the night of Sunday, January 13, 1641, the Dutch launched a final night assault on the stout fortress. About 650 Dutch soldiers - equipped with grenades, spears, cutlasses and ladders - were divided into three forces and led the charge towards the ramparts, shouting their war-cry "Help us God!". They poured through a breach in the ramparts caused by Tranquerah cannon, By 10 a.m. the next day, the Portuguese - starved, sick, wounded and out of gunpowder - surrendered and disappeared from the pages of Malay history.

To reinforce their position and influence, the Dutch made trading agreements with several states of the Malay peninsula in an effort to establish a monopoly on the trade in tin. Though treaties were established with Kedah, Ujung Salang , Bangkeri and Perak, enforcing the monopoly proved difficult.

Dutch fort, Teluk Gedung

Perak was the main tin producing kingdom in the whole peninsula and, for this reason, a Dutch garrison was established at Perak, but, in 1651, the garrison was killed and the outpost destroyed by the Malays. In 1660, even the factory established at Ujung Salang, was abandoned. Another Dutch outpost was established from 1670 to 1690 at Teluk Gedung in Pulau Pangkor.

However, like a much-wounded tiger, Melaka was never to recover her former glory again. The city's prosperity had relied on free trade - and the VOC wanted monopolies on all goods. Batavia was also the main Eastern base of the VOC and the company had no interest in developing Melaka's trade to the detriment of that of Batavia.

By the 1660s., the trade at Dutch Melaka was in serious decline and it was even rumored that the Dutch might leave the city. The Dutch usually had a garrison of only about 500 men in Melaka - and this was a port that, a century before, had been besieged by Malay forces numbering in the tens of thousands. The one factor that did cause the Dutch to remain was that they did not want Melaka to fall into any other European hands.

Johor took advantage of Melaka's decline by opening its seaport Riau to all ships and to all commerce. The Riau trade soon far surpassed that of Melaka and Johor again grew in strength. The VOC maintained its uneasy alliance with Johor, despite the competition to Melaka - the strength of Johor was seen as a safeguard to the peaceful trade in the Straits.

However, in the eighteenth century, a new power emerged that was to disrupt this precarious balance - the Bugis.

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