The man, said to be a resident of the Dutch capital, entered the Apple store on Leidseplein armed with two guns, sparking a tense five-hour-long ordeal on Tuesday.
The stand-off ended when the suspect was hit by a police car as he chased his last hostage who made a desperate break for freedom and ran out of the store.
"I can confirm that the man has died in hospital this evening," public prosecution service spokesman Franklin Wattimena said.
"More than that, we cannot say, but the investigation continues," he told AFP.
Police later hailed the hostage who helped to end the tense ordeal that gripped the city centre as a hero.
Dozens of police officers rushed to the building at 5.30pm on Tuesday (12.30am Wednesday Singapore time) after the camouflage-wearing suspect entered the store in the popular Leidseplein neighbourhood, prompting a chaotic exodus from the building.
The suspect took a Bulgarian man hostage and demanded €200 million (S$300 million) in cryptocurrency, as well as a free passage out of the city.
Around 70 people fled the building and four people hid in a closet, apparently unknown to the suspect.
'Hero role'
Five hours later, the suspect asked for water.
Footage showed the hostage bending down as the water was delivered, before running out of the building followed closely by the suspect.
The suspect was then sent sprawling by a police vehicle before a robot checked him for explosives as he lay on the road, lit up with laser sights from police snipers.
"A car from the special forces reacted very adequately and alertly," police chief Frank Paauw said in an overnight press conference, hailing the hostage's bravery.
"The hostage has played a hero role. In a few split seconds he escaped this hostage situation, otherwise it would have been an even longer night - and nasty night."
<p>This picture shows a bullet impact on the shop window of the Apple's flagship store in central Amsterdam on February 23, 2022 the day after a man with a firearm who held several people hostage in the store was overpowered after a siege lasting several hours. (Photo by Olaf Kraak / ANP / AFP) / Netherlands OUT</p>
PHOTO: ANP
Police later confirmed that the suspect was wearing an explosive device, but "that it was not primed" during the incident.
He was taken to hospital "seriously injured", police said, adding that a "wide-ranging" investigation had been launched.
"All options are open over a possible motive," they added, saying at least two homes around the Dutch capital had been searched.
Amsterdam-based daily newspaper Het Parool identified the man as Abdel Rahman A., a grocery delivery worker that has had previous brushes with the law.
However, his motive for besieging the Apple store remained unclear, Dutch media reports said.
'Prevented worse'
The suspect aimed an automatic weapon at officers, Paauw said, as special police units arrived at the scene on Tuesday and cordoned off the area around the shop.
All Apple stores across the Netherlands were closed on Wednesday, and the site of Tuesday's hostage taking will remain closed on Thursday, the company said.
<p>A man in camouflage clothing lies next to a police robot in a street after the hostage-taking ended in Amsterdam on February 22, 2022. - A man with a firearm was in the vicinity of an Amsterdam shop, police in the Netherlands said February 22, 2022 adding that officers were at the scene said by local media to be an Apple store. (Photo by Laurens Bosch / ANP / AFP) / Netherlands OUT</p>
PHOTO: ANP
Leidseplein is popular with tourists and known for its lively bars and cafes. The area was quickly closed and the restaurants, bars and theatres were shut after the hostage taking.
"Just when the city was about to reopen and return to normal life, violence is again emerging in the heart of Amsterdam," deputy mayor Rutger Groot Wassink said late on Tuesday.
Dutch Justice Minister Dilan Yesilgoz-Zegerius praised the quick action by the police.
"Their controlled and decisive action deserves nothing but compliments," she said in a tweet.