Phelps led from the start to finish the 200 fly in 1 minute, 55.70 seconds. Christophe Lebon edged fellow Frenchman Jordan Coelho to finish second in 1:59.01.
Phelps competed in the 100-meter freestyle final about half an hour later and finished eighth. Frenchman Fabien Gilot won in 48.65.
Swimming in lane one next to world champion Cesar Cielo of Brazil, Phelps took a slow start and clocked 49.70.
"I think as a whole, for the day, it's not terrible," Phelps said. "I'm more happy with my fly. I think there is still a lot of work to do." Phelps will also compete in the 200-meter freestyle and the 200-meter individual medley on Sunday.
"I will try to recover as much as I can," Phelps said.
"It's gonna be a tough day." Phelps, who turns 25 at the end of this month, holds the record for the most gold medals in a single Olympics, with eight won at the 2008 Beijing Games.
He is competing in Paris as part of his preparations for the American trials, which will determine the roster for August's Pan Pacific Championships in Irvine, California.
"I'm a bit disappointed with the race," Phelps said of the 100-meter freestyle. "It just shows where we stand right now. I know I should be a lot faster that that." Cielo finished fifth in 49.23 while American Nathan Adrian, looking to gain some more racing experience before the Pan Pacific championships, tied for second place with Yannick Agnel of France in 48.83.
Phelps added that he would try to relax by watching Saturday's World Cup football match between the United States and Ghana.
"I've got to cheer for my home country," he said.
"They've got a big match against Ghana." Olympic champion Alain Bernard of France disappointed his home crowd, failing to qualify for the 100-meter free final. Bernard posted the 18th time in the heats in 50.44.
Bernard, swimming in the same heat as Phelps, was unable to accelerate in the last 50 meters. The Frenchman, who is gearing up for August's European championships in Budapest, Hungary, said he was not worried by his performance.
"I was very tired," Bernard said. "And when you're tired, there is nothing you can do."
