Phelps was beaten again at the Charlotte UltraSwim on Sunday night, losing to Frederick Bousquet of France in the 100-meter freestyle.
Phelps touched nearly a full second behind Bousquet, world-record holder in the 50 free, after losing his first final in nearly a year. Aaron Peirsol beat Phelps in the 200 backstroke on Saturday.
Bousquet went out strong, ensuring he had a big enough lead to hold off Phelps at the end - even as the winningest Olympian ever experimented with a new straight-arm stroke that is supposed to provide more speed.
The Frenchman touched in 48.22 seconds, while Phelps never really had a chance while finishing second in 49.04.
"The biggest thing that killed me were my turns and my finishes," Phelps said. "I'm not disappointed with that time, but finish was awful. There's small things I need to work on. But overall, it was a good meet."
He was competing for the first time since capturing a record eight gold medals at the Beijing Olympics. The nine-month layoff was the longest of his career, though he had intended to come back earlier - after being photographed using a marijuana pipe, a picture that wound up on the front page of a British tabloid, he was given a three-month suspension by USA Swimming.
The sanction ended May 5, and Phelps was eager to start competing again. He entered five events at Charlotte and won the first two, the 200 free and the 100 backstroke.