Papadopoulos made his debut against Anorthosis Famagusta FC in a 3–0 away loss. He finished 2008–09 season with 22 league matches. He started the next season by scoring against ŠK Slovan Bratislava in a 0–2 away win. This was his first goal for Olympiacos. He managed to score a crucial goal against P.A.O.K. F.C. in a 1–2 away win. He also scored against AEK Athens F.C. in a 1–2 home loss. He completed 28 league appearances and he scored 2 goals. His partnership with Olof Mellberg at the centre of defence played a vital role for Olympiacos as they won back-to-back championships in the 2010–11 and 2011–12 seasons.