In March 2013, Afghanistan Cricket Board (ACB) announced that Nabi would lead the national side in the ICC Intercontinental Cup in the UAE, after Nawroz Mangal was stripped of the captaincy following his dismal show in the limited-over series in Pakistan the previous month. Under his captaincy, Afghanistan went to the 2014 Asia Cup, their first ever major international ODI tournament. During the tournament they defeated Bangladesh in just their fourth match against a Test nation. Nabi remained captain through the 2014 ICC World Twenty20 and the 2015 Cricket World Cup, but due to poor form and Afghanistan only winning one match in the World Cup, he resigned as captain in April 2015.