third round in a match which finished just before midnight on Thursday on a packed Louis Armstrong Court.
But the majority of the spectators got behind the Frenchman, who served up his trademark repertoire of leaps, bounces, flashy razor-sharp groundstrokes and smiling one-liners with the crowd.
By contrast, Isner was all business, never managing more than a discreet fist-pump to accompany a winner as the crowd opted prefereed chants of "Monfils, Monfils" rather than "Isner, Isner."
"He's a fun-loving guy and an exciting guy to watch no matter where he is playing, but honestly it was a bit surprising," said Isner, the 13th seed.
"I know the New York fans. They like to see long matches and fifth sets, but I was a little disappointed. Not going to sugar-coat it. If I was playing him in France, it certainly wouldn't be like that."
He added: "I didn't want to get involved in a hit-and-giggle match. I just wanted to stay focused. I didn't want to be too friendly out there."
Isner's frustration reflected the pressure he is under as he attempts to become the first American man since Andy Roddick at the US Open in 2003 to win a Grand Slam title.
"I had a similar match at the French Open against Tommy Haas in Paris. I had about five people cheering for me and those were the five people in my box. So the French people there were cheering for a German," he said.
"I could say something else, but I'm not going to."
Monfils was delighted by the atmosphere.
"It was good. I love playing here and the New York crowd has always responded well to me. It was a great occasion," he said.
Isner will be testing the patience of the home crowd again in the next round when he meets Germany's Philipp Kohlschreiber.
Last year, the pair also played each other in the third round with the German winning in five sets in a match which ended at 2:26 a.m., tying the tournament record for the latest finish.
"It's crazy, playing him in the third round again. Last year was disappointing, but he's been so solid for so long now," said the 28-year-old.
If Isner gets past the 22nd-seeded Kohlschreiber, he is likely to face world number two Rafael Nadal in the fourth round.