On 11 August 2013, Mannus sustained a shoulder injury during a match against Kilmarnock, which ruled him out for six weeks. He came back from his injury earlier than expected, making his return on 14 September 2013, in a 2–1 loss against Hibernian. On 18 January 2014, Mannus was sent-off, along with Ryan Stevenson of Hearts after they were involved in an alteration "following an angry goalmouth melee". He would miss one match after the club decided against appealing the sending off. While serving his suspension, Mannus fractured a bone in his thumb, which was expected to keep him out for six to eight weeks. However, he made his return to the side after only two weeks, on 16 February 2014, as St Johnstone lost 3–0 against Celtic.
