As he was not greatly interested in school, Cronin's grades improved only when the San Francisco Seals of the Pacific Coast League began giving away tickets to students with good conduct and attendance.

Red Sox farm system director Billy Evans thought he had found Cronin's successor in Pee Wee Reese, the star shortstop for the Louisville Colonels of the Triple-A American Association.

Believing he still had enough left to be a regular player, Cronin deliberately downplayed Reese's talent and suggested the Red Sox trade him.

Even when World War II saw many young players either enlist or drafted in the armed services, Cronin limited his playing appearances to cameo roles as a utility infielder and pinch-hitter.

At the end of the 1947 season, Cronin succeeded Eddie Collins as general manager of the Red Sox and held the post for over 11 years, through mid-January 1959.

[4] In his first off-season, he acquired shortstop Vern Stephens and pitchers Ellis Kinder and Jack Kramer from the St. Louis Browns; all played major roles for the 1948 Red Sox, who finished the season tied for first place with the Cleveland Indians but lost a tie-breaking playoff game against the Indians for the AL pennant.

With the exception of Ted Williams (who missed most of the 1952–1953 seasons while serving in the Korean War), the core of the 1946–1950 team aged quickly and the Red Sox faced a significant rebuilding job starting in 1952.

Cronin's acquisition of future American League Most Valuable Player Jackie Jensen from Washington in 1954 represented a coup, but the club misfired on several "bonus babies" who never lived up to their potential.

[4] By the end of Cronin's eleven-year term as general manager, the Red Sox were the only major-league team that had not fielded a black player.

[13] During this time, he reportedly made unsuccessful efforts to integrate the team, including attempts to sign or trade for Bill Greason, Larry Doby and Charlie Neal.

Notably, in 1949, he sent scout Larry Woodall to evaluate an 18-year-old Willie Mays of the Birmingham Black Barons of the Negro American League.

[19] Finally, in the middle of 1959, both were promoted from the Triple-A Minneapolis Millers by Cronin's successor, Bucky Harris: Green became the first African-American to play in a major league game for the Red Sox on July 21; one week later, Wilson became the second, and their first black pitcher.

The league also underwent four franchise shifts: the relocation of the original Senators club (now owned by Cronin's brother-in-law and sister-in-law, Calvin Griffith and Thelma Griffith Haynes) to Minneapolis–Saint Paul, creating the Minnesota Twins (1961); the shift of the Athletics from Kansas City to Oakland (1968); the transfer of the Pilots after only one season in Seattle to Milwaukee as the Brewers (1970); and the transplantation of the expansion Senators after 11 seasons in Washington, D.C., to Dallas–Fort Worth as the Texas Rangers (1972).

Two of the charter members of the old eight-team league, the Chicago White Sox and Cleveland Indians, also suffered significant attendance woes and were targets of relocation efforts by other cities.

[23] In 1973, Cronin's final season as league president, the NL attracted 55 percent of total MLB attendance, 16.62 million vs. 13.38 million total fans, despite the opening of Royals Stadium in Kansas City and the American League's adoption of the designated hitter rule, which was designed to spark scoring and fan interest.

In an interview with Larry Gerlach, Ashford stated, “Jackie Robinson had his Branch Rickey, I had my Joe Cronin.” [24][25] After the 1968 season, Cronin drew headlines when he fired AL umpires Al Salerno and Bill Valentine, ostensibly for poor performance; however, it later surfaced that the two officials were fired for attempting to organize an umpires' union.