Ertuğral's, coaching career began in 1990 with German amateur side TSV Dagersheim, he then managed from 1991 to 1995 TSV Plattenhardt. Ertuğral also coached Congo DR, then still known as Zaire, taking them to the African Cup of Nations in 1996, where they were eliminated in the quarterfinals. It was that performance with Zaire which caught the attention of Kaizer Chiefs. He then worked as assistant manager for Turkish sides Gençlerbirliği and Trabzonspor in the late 1990s.
Ertuğral took Ajax Cape Town to ABSA Cup glory with a 2–0 victory against league champions Mamelodi Sundowns on May 26, 2007. That proved to be a successful season for Ajax under Ertuğral as they went on to finish fourth in the league and the only side never to suffer defeat against Sundowns in that season.
He picked up a number of trophies with South African club Kaizer Chiefs during his first stint, including the African Cup Winners' Cup in 2001, being the only person to lead a South African team to this honour.
On 24 April 2013 it was announced that Muhsin Ertuğral would take over as the new Technical Director of Ajax Cape Town F.C.. This decision resulted in the direct resignation of then interim coach Jan Versleijen, who had not been notified of the new hiring. As a result Muhsin Ertuğral will see the Cape club through until the end of the 2012-13 PSL season.David Nyathi was announced as his assistant coach, who had previously lead the Ajax CT under-19 team to the 2013 Metropolitan Premier Cup Championship, where he won the “Coach of the Tournament Award”.