In 2013, Misbah was brilliant in terms of his batting. He moved to a career-best seventh place in the ICC rankings for ODI batsmen. Misbah was the leading run scorer in ODI cricket with 1373 runs for year 2013 ahead of Mohammad Hafeez and Virat Kohli. He also had 15 ODI half centuries, which is a record for most ODI half centuries in a calendar year, as well as hitting 3rd most ODI sixes that year.
Despite, Pakistan losing all 3 of their games, h was named as part of the 'Team of the Tournament' in the 2013 Champions Trophy by the ICC. He was also named as captain of the Team by Cricinfo.
In 2013, Pakistan played bilateral series against South Africa, India, West Indies, Zimbabwe and Sri Lanka and they also participated in Champions Trophy. Despite winning against India in India, away series lose against South Africa 3–2, win-less streak in Champions Trophy and winning against minnow Zimbabwe 2–1 and then again defeat in home series against South Africa in UAE 4–1 put huge criticism on Misbah's captaincy and his approach to the game. Especially series defeat against South Africa 4–1, brought Misbah's captaincy under severe scrutiny. Ex-Pakistani players were demanding a total renovation of Pakistan cricket, and Misbah was being criticized for his captaincy, slow batting and the defeat. The PCB, however, announced that Misbah was to remain captain until the 2015 Cricket World Cup. Several TV shows and notable personalities opposed this decision and demanded that Misbah should be sacked.