As in his first year, Silva struggled for minutes in 2008–09. He played his first match on 22 November 2008 in a 1–0 league defeat of Associação Naval 1º de Maio, playing 16 minutes off the bench. He made his first start in a 3–0 home win against Marítimo in the Taça da Liga, and he also made Bento's starting XI three months later in the "Lions"' 1–7 loss to FC Bayern Munich in the Champions League last 16 second leg. He made 19 appearances in all competitions, notably playing the full 90 minutes in home wins against of C.F. Estrela da Amadora and C.D. Nacional.