The man, said to be a resident of the city, entered the Apple store on Leidseplein armed with two guns, sparking a five-hour siege on Tuesday.
The standoff ended when the suspect was hit by a police car as he chased his last hostage who ran out of the store.
“I can confirm that the man has died in hospital this evening,” said Franklin Wattimena from the public prosecution service. “More than that, we cannot say, but the investigation continues.”
Police earlier 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 after the camouflage-wearing suspect entered the store in the popular Leidseplein neighbourhood, prompting people to flee.
The suspect took a Bulgarian man hostage and demanded €200m worth of cryptocurrency, as well as free passage out of the city.
About 70 people fled the building and four people stayed hidden from him in a closet.
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 hit by a police car before a robot checked him for explosives as he lay on the road lit up with lasers from police snipers.
“A car from the special forces reacted very adequately and alertly,” said Frank Paauw, a police chief. “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.”
The suspect had 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.
Police confirmed that the suspect was wearing an explosive device but that “it was not primed” during the incident. The man was taken to hospital “seriously injured”, police said, adding that a wide-ranging investigation had begun. “All options are open over a possible motive,” they added, saying that at least two homes in the Dutch capital had been searched.
All Apple stores across the Netherlands were closed on Wednesday. The site where the hostages were taken would remain closed until Thursday, the company said.
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 situation. The incident happened close to where well-known Dutch crime reporter Peter R de Vries was gunned down in 2021.
Amsterdam’s deputy mayor, Rutger Groot Wassink, said late on Tuesday: “Just when the city was about to reopen and return to normal life, violence is again emerging in the heart of Amsterdam.”
The Dutch justice minister, Dilan Yeşilgöz-Zegerius, praised the quick action by the police. “Their controlled and decisive action deserves nothing but compliments. It prevented worse.”