Fernandes made his debut for the club, starting the match and played 81 minutes before being substituted, in a 3–0 win against SC Kriens on 3 February 2013. Since joining FC Sion, he quickly became the club's first team regular for the rest of the season. However, towards the end of the season, Fernandes faced restrictions, as he faced suspension on two occasions and suffered an injury that will keep him out for the remainder of the 2012–13 season. At the end of the 2012–13 season, Fernandes made sixteen appearances in all competitions. Following this, his options to join FC Sion permanently has ended after the club have to pay the price to sign Fernandes.