Shittu made his second Millwall debut the next day on 11 April 2017 against Crawley Town in the first round of League Cup, where he came on as a substitute in the second half and played throughout extra time, leading to penalty shootout, as a result, Millwall went on to lose 4–1. After a rough start, having appeared as an unused substitute, Shittu regained his first team place and was then given a captaincy in absence of both captains Robinson and Trotter, in a match against Bristol City, which saw them draw 1–1 on 2 October 2012. In a 2–1 win over Bolton Wanderers on 6 October 2012, Shittu's performance throughout 90 minutes resulted him being named Man of the Match by the supporters. From that moment on, Shittu captained the side throughout the 2012–13 season and helped the side go 12 game unbeaten run along the way. On 25 January 2013, in the fourth round of the FA Cup, Shittu scored his first Millwall goal, in a 2–1 win over Aston Villa. On 13 March he scored the only goal, a header away to Blackburn Rovers to put Millwall into the FA Cup semi-final against Wigan Athletic at Wembley Stadium. Despite being sidelined twice, due to injury and suspension during the season Shittu finished the 2012–13 season, making forty–four appearances and scoring two times in all competitions. For his performance, Shittu was also voted player of the year for 2013. In addition, Shittu signed a two–year contract with the club, keeping him until 2015.
