In between his playing and managing careers, Rodgers served as a coach for the Minnesota Twins (1970–74), San Francisco Giants (1976), and the Brewers (1978–80). He managed in the Angels' farm system in 1975 and 1977. His managerial career was book-ended by unusual circumstances.
He first became manager of the Brewers (then contenders in the American League East Division) on an acting basis at the outset of the 1980 season. He was serving as the club's third-base coach when pilot George Bamberger suffered a heart attack. Rodgers posted a record of 27–21 as acting field boss until Bamberger was able to return. However, with the Brewers treading water under Bamberger with a record of 47–45, the manager stepped down in September and Rodgers resumed the helm, the team winning 13 of its last 23 games to ultimately finish third. The 1981 campaign was disrupted for six weeks by an in-season players' strike, which caused the major leagues to adopt a split-season format. Rodgers led the Brewers to the best overall record in the AL East at 62–47 and the second half title, but Milwaukee lost the divisional playoff to the New York Yankees, three games to two. It would be Rodgers' only postseason appearance as a manager. In 1982, the Brewers started slowly under Rodgers and he was fired in May with the team's record a poor 23–24. The Brewers then caught fire under his successor, batting coach Harvey Kuenn, to finish with 95 wins and went on to win its only AL pennant as "Harvey's Wallbangers."
After guiding the Indianapolis Indians of the AAA American Association to the 1984 regular season championship, Rodgers was promoted to manager of the parent Expos, replacing Jim Fanning. His first six years (1985–90) in Montreal were largely successful, with the Expos averaging almost 84 wins per season, but when the team faltered in 1991, winning only 20 of its first 49 games, Rodgers was replaced as manager by Tom Runnells.
He was not out of work long. In August 1991, the Angels fired Doug Rader and hired Rodgers as their new pilot. Buck – still well liked from his playing days in Anaheim – led the Halos to a 20–18 record for the remainder of the campaign, and was 39 games into his first full season as Angel manager in 1992 when a bus carrying the California club was involved in an expressway accident; Rodgers was seriously injured and missed almost 90 games. He returned, but still felt the after-effects of his injuries. Perhaps more damaging, the Angels did not respond to his leadership. They posted a losing mark in the final weeks of 1992, finished 20 games below .500 in 1993, and were only 16–23 in May 1994 before Rodgers was replaced by Marcel Lachemann.