His talent would not go unnoticed, and in 1964 Nuninga transferred over to Ajax. He was an integral part of what is considered the great 'blooming' period of the Amsterdam club. He participated in the 1968-69 European Cup, as the first choice striker for Ajax, and started in the Final, where Ajax would face, and eventually lose to AC Milan (4-1). After this loss, Nuninga was sidelined by then coach Rinus Michels.