At the beginning of 2009, there was speculation over Mohammad Ashraful’s position as captain after a succession of defeats for Bangladesh and a run of poor form for Ashraful. Shakib was considered as a possible successor by the Bangladesh Cricket Board (BCB). However, the BCB was cautious of over-burdening the all-rounder and decided against the move. Other candidates were discounted, and Ashraful remained as captain. Later in 2009, Ashraful’s captaincy was again under scrutiny after Bangladesh exited the 2009 ICC World Twenty20 in the first round as a result of being defeated by Ireland and India. When Mashrafe Mortaza replaced Mohammad Ashraful in June 2009, Shakib was appointed vice-captain, filling the position vacated by Mortaza.
In July–August 2009, Bangladesh toured the West Indies. When Mortaza injured his knee in the first Test, he was unable to take to the field on the final day and Shakib took over as captain. He and Mahmudullah led Bangladesh’s bowling attack, sharing 13 wickets in the match and securing a historic win for Bangladesh. It was Bangladesh’s first against the West Indies, their first overseas Test victory, and only their second Test win. The West Indies side was very inexperienced due to the fallout of a dispute between the West Indies Cricket Board and the West Indies Players’ Association over pay. The first XI had made themselves unavailable for selection and a new squad had to be chosen. Seven West Indies players made their Test debut in the match and the side was captained by Floyd Reifer who had played the last of his four Tests ten years earlier