Hopper joined the Brooklyn Dodgers organization in 1942. He managed the Mobile Bears of the Southern League in 1945, leading them to the league championship. He was promoted to become the manager for the Montreal Royals of the International League for the 1946 season. That year, Jackie Robinson, the first black player to integrate baseball since the 1880s, entered the Dodgers farm system and was assigned to the Royals. Hopper, who opposed integration of baseball at the time, asked Branch Rickey, the general manager of the Dodgers, to assign Robinson to a different Dodgers affiliate, but Rickey kept Robinson assigned to Montreal. Robinson reported that Hopper treated him well, and the Royals won the Governors' Cup as the International League champions. The "Sporting News" named Hopper the Manager of the Year for all of minor league baseball that season. Hopper recommended the Dodgers promote Robinson to the major leagues for the 1947 season.