In April 1944, McManus was hired to manage one of the clubs in the All-American Girls Professional Baseball League. He began his career in the league as the manager of the Kenosha Comets. He managed the Kenosha squad to the first half championship and lost to Milwaukee in the playoffs. In January 1945, McManus announced that he would return to Kenosha, having rejected an offer to return to men's baseball. He noted: "It is a lot of fun managing those girls. They know how to play the game, catch signals in a hurry and put everything they have into their play." He ended up as manager of the South Bend Blue Sox of the All-American Girls Professional Baseball League in 1945. In 1946, he managed the Chicago Bloomer Girls.