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.