 Markarian coached Universidad de Chile in 2009, winning the Chilean Torneo Apertura- the first title the Universidad de Chile had won in the last 5 years- before then terminating his contract due to differences with the club's management only six months into the year.On July 2010, Markarian was appointed as the new head coach of the Peru national team for the 2011 Copa America and the 2014 FIFA World Cup Qualifiers.Markarian succeeded José del Solar who led the Peruvian team in a disastrous campaign, finishing last during the 2010 World Cup qualifiers.