Matthews served as general manager of the Chicago Cubs for seven full seasons and became one of the first front-office employees in the history of the New York Mets in 1961, the year before they began play in the National League.

As Brooklyn's top scout in the Midwest, Matthews was one of multiple Dodger evaluators who followed Jackie Robinson of the Kansas City Monarchs of the Negro leagues in 1945.

During his seven seasons (1950–56) as the top baseball official in the Chicago front office, Matthews was able to break the Cubs' color line, signing Ernie Banks as the team's first African-American player.

However, plagued by a poor farm system and not aggressive enough in the signing of other black and Latin talent, the Cubs could not escape the NL's second division during Matthews' reign.

He held the identical title he did with Chicago, but in his new post he served as assistant GM to John J. Quinn, the Braves' incumbent general manager.