On 20 September 2013, Clemente was named manager of Libya, taking over from Abdul-Hafeedh Arbeesh who was fired after a 0–1 defeat to Cameroon for the 2014 World Cup qualifying campaign. He led the nation to its first silverware, the 2014 African Nations Championship, with a penalty shootout win over Ghana in the final in Cape Town. However, he later failed to qualify for the 2015 Africa Cup of Nations and 2016 African Nations Championship as the defending champions. He was later dismissed following a 4-0 loss against DR Congo in the 2018 World Cup qualifiers in 2016.