After two years as a graduate assistant coach for the University of Tennessee Volunteers he began his managerial career in 1990, taking over the Miami Miracle of the Florida State League.

He was chosen to be the first coach to instruct the first Marlins prospects of the franchise assigned to the Erie Sailors minor league team.

González coached throughout the Marlins organization, including a 1997 stop as manager of the Portland Sea Dogs, the Double–A Eastern League affiliate of the Marlins; he managed the Sea Dogs to a first-place finish in the Eastern League's Northern Division, with a record of 79–63.

González was named as a coach for the 2007 NL All-Star Team, replacing Willie Randolph who was undergoing shoulder surgery.

[9][10] On October 13, 2010, González was officially named the new manager for the Atlanta Braves, succeeding the retiring Bobby Cox.

[11] In his first season managing the team, he led the Braves to an 8+1⁄2-game lead in the National League Wild Card race on August 26, only to suffer a historic collapse and lose the spot to the eventual World Series champion St. Louis Cardinals on the final day.

It was a 6–3 loss to the St. Louis Cardinals in the 2012 National League Wild Card Game at Turner Field.

González put this game under protest after the infield fly rule was called by umpire Sam Holbrook on a ball that fell in shallow left field in the bottom of the eighth inning.