Amanatidis was born in Kozani, Greece. His family immigrated when he was nine years old to Stuttgart where he joined SC Stuttgart. Two years later he went to VfB Stuttgart academy. In 2002, he started his Bundesliga career having already played on loan for Greuther Fürth in lower divisions. After a clash with then VfB Stuttgart coach Felix Magath over his lack of opportunities he was given on loan to struggling Bundesliga side Eintracht Frankfurt where he impressed despite the eventual relegation of the team to second division.