“I am happy and excited about this deal. It’s a new chapter, a new challenge. There was interest 10 years ago, but some things are also a matter of timing and now was the time,” said 51-year-old Coleman.
Atromitos are currently fighting to stay in the Super League where they sit in 13th place in the 14-team championship with just nine points after 15 matches.
Coleman is expected to arrive on Sunday in Greece together with his assistant Kit Symons, who will remain as assistant coach of the Welsh national team.
Coleman played for Swansea City, Crystal Palace, Blackburn Rovers and Fulham while making 32 appearances for the Welsh team.
In his coaching career, he famously led Wales to the semi-finals of Euro 2016.