The 2012–13 season saw Naoupu play fewer games in total, but put in several strong performances. He played 14 games in the 2012–13 Pro12, starting all but one, and scoring four tries. Over the course of the season, Naoupu faced competition from Academy graduate Eoin McKeon for the number 8 position. In the 2012–13 Heineken Cup, he started two games and came on as a replacement in another. In January 2013, it was announced that Naoupu had been offered a contract extension on the back of his good form, agreeing a deal to stay with Connacht until the end of the 2014–15 season.