A passer-by signalled the gruesome scene to police, who linked it to the discovery of a decapitated body in a burnt-out car elsewhere in the city.
Police said the body belonged to 23-year-old Amsterdam resident Nabil Amzieb, who was known to the authorities.
"A police probe later confirmed the head belonged to the body," they said in a statement.
The hookah bar called the Fayrouz Lounge is a "well-known gathering spot for criminals involved in the so-called "Mocro-war", a power struggle mainly between Moroccan gangs in the city, public broadcaster NOS said.