The man, 32, thought to be called Anis B., was detained on Sunday suspected of receiving orders from ISIS to attack targets in France along with Reda Kriket, who was detained near Paris last week.
"During the search, phones, SIM cards, hard drives, cash, ammunition and drugs were seized," a spokesman for the Dutch prosecutor, Wim de Bruin, told AFP.
No explosives were found during the raid in which a total of four men, including two suspects of Algerian background, were arrested, he added.
Anis B is expected to be handed over to France after an extradition hearing at an Amsterdam court, de Bruin said, although no date has yet been set.
The Netherlands was already on heightened alert after the airport and metro attacks in Brussels last Tuesday, with security stepped up at airports and train stations and border controls tightened.
French police said they had thwarted an attack by 34-year-old Kriket after arresting him on Thursday and discovering several assault rifles and explosives in an apartment in a Paris suburb.
French Interior Minister Bernard Cazeneuve said that a planned attack at "an advanced stage" had been foiled, without giving further details.
Belgian police at the weekend charged two men with involvement in a terrorist group over the foiled French plot linked to Kriket.
Kriket was convicted in absentia last year in Belgium in the trial of a jihadist network linked to Syria in which one of the defendants was Belgian Abdelhamid Abaaoud, thought to be the ringleader of the November attacks in Paris.
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