Wenger left Arsenal after 22 years at the helm earlier this summer and was replaced at the Emirates Stadium by Emery, who steered Paris Saint-Germain to the domestic treble last season.
Iwobi was just five months old when Wenger was appointed as Arsenal boss, and went on to feature in almost 100 senior games for the club under the Frenchman.
"I was surprised by his decision. [Wenger] has been there for me since I joined the club and has been very inspirational and influential on my career, but I am excited having our new manager (Emery) next season," Iwobi wrote in his programme notes prior to Nigeria's friendly with England on Saturday.
"It has always been my childhood dream [to play for Arsenal]. I have been playing for Arsenal since I was six. The fact I am representing them now is like a dream come true. I am always proud to wear the Arsenal colours and long may it continue."
Iwobi - who represented England at youth level - has been included in Nigeria's squad for this summer's World Cup.