McInnes joined Liverpool's administrative staff after he retired in 1946. He was Liverpool's Secretary from 1955 until he took his own life on 5 May 1965, the day after the famous 3-1 win over Inter Milan at Anfield in the semi-finals of the European Cup. Four days earlier Liverpool had won the FA Cup for the first time against Leeds at Wembley. Apparently McInnes had been overwhelmed by the size of his task at Liverpool resorting to sleeping on a camp bed at Anfield. McInnes had been seen at the ground pulling at some cord earlier in the day, seemingly in quite good humour, but was later found hanging from a beam at the rear of the Kop.

Bill Shankly worked with McInnes for five and a half years at Liverpool and got to know him quite well. "Jimmy was honest and he was also quick-tempered. Sometimes he could be rude to people – some of them needed it, and he was right – but he would be gentlemanly with people he respected," Shankly revealed in his autobiography. "There were some of us at Anfield with whom he never had a harsh word. Others would find him difficult to deal with and hard to understand. I’ve heard him calling somebody on the telephone and suddenly, bang! The phone would go down. Jimmy loved a game of snooker, and he was a good player. It was a change from his chores as Secretary. When the club began to be transformed, Jimmy got the lash of the success. There were only a few seats in the stand in those days and when we won the Second Division championship, reached the FA Cup semi-final, won the First Division championship and then won the Cup, Jimmy’s work was doubled and everything began to pile up on top of him. He needed help."