Last week, Triple-A manager Wally Backman told SNY's Toby Hyde that Puello would be away from the team for a few days and return to action Friday, which he did.
ESPN has reported that a federal grand jury in Miami is looking into charges against Biogenesis founder Tony Bosch.
Puello, 23, served a 50-game suspension last year for his involvement with Biogenesis.
Puello was signed a non-drafted free agent in 2007. He was ranked No. 14 among Mets prospects by MLB.com entering the 2013 season.
He is hitting .248 with .309 OBP, four extra base hits, seven RBI and 21 strikeouts in 30 games with Triple-A this season.