Pennock became the general manager of the Charlotte Hornets, a Red Sox' farm team of the Piedmont League, prior to the 1935 season. He returned to the Red Sox in 1936, serving as the first base and pitching coach under manager Joe Cronin. He served in this role through the 1938 season. In 1939, Pennock served as the assistant supervisor of Boston's minor league system, reporting to Billy Evans. Pennock succeeded Evans as Director of Minor League Operations late in the 1940 season.