In July 2009, Mathys moved to Swiss Challenge League club FC Biel-Bienne on a free transfer.
He made his league debut for the club on 26 July 2009 in a 2–0 loss to FC Vaduz.
[2] He scored his first league goal for the club a week later in a 3–0 home victory over Stade Nyonnais.
He made his league debut for the club on 24 July 2016 in a 1–1 draw with FC Thun.
[7] His first league goal came as part of a hat-trick scored in a 5–1 victory over FC Lugano.