Arsenal battled back from a couple of goals down to level up the match at 2-2 before the interval, but they were second best after the restart and fell to a late Marcos Alonso strike.
Iwobi insists that he and his teammates gave their all for Emery, though, and has acknowledged that it will take time before the hard work begins to show.
"We started shaky. I don't know why - maybe we didn't know what to do, but we picked ourselves up and got going," he told BT Sport. "Unfortunately we weren't able to take all our chances.
"We were on a high at half time. The message [from Emery] was to keep it going, keep our head and don't lose ourselves. We fought hard for him.
"We enjoy training, everyone is buying into his ideas. It all takes time, a new manager, a new system and the fans and players know that."
Emery is the first Arsenal manager to lose his first two games since Steve Burtenshaw, who lost his first three in charge as caretaker in March/April 1986.