He managed Peru in a successful 2011 Copa América campaign with the team finished third after beating Venezuela 4–1, leaving fans to be enthusiastic about a possible football revival for Peru. However, the 2014 World Cup qualification became another disappointing campaign, with the loss 1–2 of Peru over his home ancestral team Uruguay in Lima meant that the Peruvians would miss another World Cup. In October 2013, Markarián resigned as head coach of the Peru National Team after failed to help Peru to qualify for the 2014 FIFA World Cup. Peru would eventually qualify for World Cup four years later.