Phelps, competing first time following a six-month ban for a drunk driving conviction, flashed his old form on Thursday when he won the 100 metres butterfly in the Arena Pro Swim Series meet.
But on Friday, the 18-times Olympic gold medalist could only manage 17th in the 400 freestyle after a time of 4 minutes, 2.67 seconds kept him out of the main final.
Phelps' time put him in the C final but he elected not to swim it and also pulled out of his scheduled 100 metres backstroke race in the evening.
While it was not the result he was looking for, Phelps was swimming the freestyle for the first time since 2009 and said he saw it as a personal challenge.
He spent the rest of the evening working in the television booth as he will now turn his attention to Saturday's 200 individual medley and 100 freestyle events.
Phelps is competing for the first time since last August with an eye toward returning to glory at the 2016 Olympic Ga

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