Early career, Toronto Blue Jays, and Atlanta Braves

His playing days cut short by a shoulder injury, Williams began his minor league managing career with the California Angels in 1974. He soon reached the Triple-A level and was appointed the third base coach of the Toronto Blue Jays in 1980.

Williams remained as Toronto's third base coach for six seasons, until he was promoted to manager in 1986 when Bobby Cox left the organization to rejoin the Atlanta Braves. He was the Blue Jays' manager until the 1989 season, when he was fired May 14 and replaced by Cito Gaston after the team got off to a 12–24 start. Gaston went 77–49 for the rest of the season and won the American League East title. Williams finished with a record of 281 wins and 241 losses.^[2]

He spent 1991–96 with the Atlanta Braves as their third-base coach, working again under Bobby Cox, including the Braves 1995 World Series championship season. While with the Braves, Williams developed a reputation as an outstanding teaching coach, especially adept at working with infielders.

During the 1992 National League Championship Series, he waved home Sid Bream after seeing Barry Bonds having to make a difficult throw on a single while the game was tied in the ninth inning. Bream made the slide that would win the pennant for the Braves in that game.

Boston Red Sox

On November 19, 1996, Williams was hired by the Boston Red Sox; the team had fired Kevin Kennedy immediately after the season ended, and Williams was hired by general manager Dan Duquette after a lengthy search that saw many names considered (such as Grady Little and Whitey Herzog).^[3]

The 1997 team was hindered by injuries and went 78-84. The following year, they went 92-70, which was good enough for second best in the American League and a wild-card spot. They lost to the Cleveland Indians in the Division Series.

In 1999, the Red Sox went 94-68 and clinched a wild card spot again. On August 14, Williams, having seen ace Pedro Martinez arrive late for his scheduled start, elected to not let him pitch in the game despite the objections of Martinez. Nine innings later, Martinez had received the win after being called to pitch in the 6th inning and threw four innings in relief.^[4] The Sox reached the American League Championship Series after beating the Indians in an ALDS rematch, but lost to their arch-rivals, the New York Yankees in five games. Williams received the 1999 Major League Baseball Manager of the Year Award for the American League.^[5]

Williams' relationship with general manager Dan Duquette soured, with players such as Carl Everett also having disagreements with Williams, who liked to constantly change the batting lineup for games. Williams developed a feud with Everett, which saw Duquette back Everett publicly in the late stages of the 2000 season, which saw them go 85-77 and miss the playoffs handily. The ensuing disagreement soured the already tense dynamic between Williams and Duquette, to the point where team CEO John Harrington had to call a meeting between Williams and Duquette to try and smooth things over.^[6][7]

When the Red Sox — depleted by injuries — slumped in August 2001, Duquette fired Williams. The club then lost 27 of 43 games under Duquette's appointee, Joe Kerrigan. Williams finished his tenure as Red Sox manager with a record of 414 wins and 352 losses.^[2]

Houston Astros and Philadelphia Phillies

On November 1, 2001, Williams was hired to become manager of the Houston Astros.^[8] The other reported candidates were Jim Fregosi and Tony Pena. The Astros went 84-78 in 2002 and were not a particularly serious threat that season. At one point in his tenure, he apparently came up with a suggestion to name the foul poles at Minute Maid Park "fowl poles" and do branding with chicken restaurants. As it turned out, the Astros would do a partnership with Chick-fil-A to brand the poles as such in 2006, which as of 2023 is still present on the poles at the park. He made it clear to owner Drayton McLane that he was not particularly interested in playing ball with the media, which in turn led to a perception of him being distant, although it was said that Williams was quite friendly when talking about baseball rather than off-the-field issues. The Astros fell short by one game for the NL Central title to the Chicago Cubs in 2003, losing six of their last nine games. However, expectations were raised in the offseason when ownership signed pitchers Roger Clemens and Andy Pettitte. The 2004 season did not get off to a great start for Williams, and they went into the All-Star break at 44-44 after losing five of seven games in their last road trip before returning to Houston for the break. Williams was assigned to serve as a National League coach at the 2004 All-Star Game, held in Houston. When he was announced to the crowd at Houston's Minute Maid Park, he was greeted with jeers; the next morning, general manager Gerry Hunsicker fired him, citing the past week as a turning point. Hunsicker was quoted as saying, "The message we wanted to send is that we needed a dramatic change. The more new faces, the more new energy that we can bring in here, the greater impact we might make. My biggest regret was the fact that this week couldn't have been any more awkward for all of us. "The unfortunate reaction he got from the fans, and the speculation that became rampant in the last day or so was very unfortunate. He deserved better."^[9]

He was replaced by Phil Garner, who Hunsicker had contacted about taking the job earlier.^[10] Garner would lead the Astros to the 2004 National League Championship Series, but they fell one game short of going to Houston's first ever World Series (the following year, Garner led the Astros to the World Series). Williams finished with a record of 215 wins and 197 losses.^[2] Williams described his tenure as one where he felt bad about not making the playoffs while stating, “We just couldn’t hit a lick that season. Remember? We couldn’t have hit if we’d gone up there with a banjo. We just couldn’t get anything going. And it was about three weeks after I left that they finally started playing well. Those things happen.”^[11]

On October 16, 2006, Williams was named the Philadelphia Phillies bench coach^[12] and continued with that role through the Phillies 2008 World Series championship season. Williams decided not to return to his position for the 2009 season. Phillies manager Charlie Manuel said, "As far as I know, it's not like that he left on a bad note."^[13]

Managerial record

As of February 13, 2014