Lewandowski was head coach of VfL Bochum II between 1 July 2006 to 31 December 2006.
Lewandowski was appointed as head coach of Bayer Leverkusen in April 2012 alongside Sami Hyypiä. After the 2012–13 season, Lewandowski went back to the youth set–up, leaving Hyypia as the sole head coach of the first team. Hyypiä took sole charge of the team on 24 June 2013. Lewandowski became the interim head coach of the first team after Sami Hyypiä was sacked.