The under-fire Spaniard admits his Arsenal players lack confidence but insists they are better than recent form suggests and he hopes to get the chance to help them turn things around.
The 2-1 loss extended a run of seven games without a win for the Gunners and heaped even more pressure on Emery.
Pierre-Emerick Aubameyang's first-half strike had Arsenal on course for a morale-boosting win in front of a sparse Emirates Stadium crowd.
But Frankfurt rallied and left north London with a win courtesy of Daichi Kamada's nine-minute brace.
Banners were displayed calling for Emery to leave as other names continue to be linked to the post but the beleaguered Spaniard seems keen to battle on despite the latest damaging result.
"Now our moment is not good," he said. "We need to win and we need to gain confidence. I think we are better than we are showing, everybody, the players, the coaches and me.
"Now we lost some confidence and we need to win. I can understand the criticism about the team, about me. We are not in a good moment and also as a coach, I had that moment also in my career."
Frankfurt offered very little in the contest and scored twice from their four shots on target as Emery felt his below-par side were unfortunate to lose.
He felt they deserved much more from the game, but that will not wash with the Gunners fans, who are demanding a change.
Despite the defeat, Arsenal are all-but through to the knockout stages and would need to lose by five goals at Standard Liege next month to fail to qualify.
Attention will now turn to this Sunday's game at Norwich, and if Emery is still in charge, he will desperately need all three points to take the pressure off.