Baker's coaching career started as a first base coach for the San Francisco Giants in 1988, and then he spent the following four years (1989–1992) as the hitting coach, and finally became the manager in 1993, replacing the departing Roger Craig. In his first year as Giants manager, he won the NL Manager of the Year award, leading the team to a 103–59 record, which was the second-best record in baseball that year (behind the 104–58 Atlanta Braves), and 31 games better than their 72–90 finish the previous year. His Giants went on to win division titles in 1997 and again in 2000; Baker would win Manager of the Year honors in both of those years as well. It was during his San Francisco tenure that the term "Dustiny" was coined by former Giants pitcher Rod Beck.