He was most recently the manager of Swiss Super League side Grasshopper Club Zürich, whom he saved from relegation.

In 1999, he became head coach of BSC Young Boys, with whom he led the 2001 resurgence in the National League A and 2002 in the UEFA Cup.

[4] On 17 May 2010, Marco Schällibaum took over as interim coach at FC Lugano for the Axpo Super League season 2009–10.

[6] After leaving FC Lugano he was hired as a FIFA coaching instructor in Qatar, Mongolia and South Korea.

On 10 April 2024, he was appointed as the new head coach of Grasshopper Club Zürich, also in the Swiss Super League.

He took over Grasshoppers in a time of crisis, as the team had slipped to the second to last place in the league with only two games won in 2024.

Most importantly, he successfully managed Grasshoppers to a victory over FC Thun in the relegation play-off,[20] helping them remain in the Swiss Super League.