Jackson was hired as assistant coach for the Bulls in 1987, and promoted to head coach in 1989. It was around this time that he met Tex Winter and became a devotee of Winter's triangle offense.[8][9] Over 9 seasons, Jackson coached the Bulls to 6 championships in impressive fashion, twice winning three straight championships over separate three year periods. The "three-peat" was the first since the Boston Celtics won eight titles in a row from 1959 through 1966.

Jackson and the Bulls made the playoffs every year, and failed to win the title only three times. Jackson lost in his first season in 1990. Michael Jordan's first retirement after the 1993 season marked the end of the first "three-peat," and although Jordan returned just before the 1995 playoffs, it was not enough to prevent a playoff exit to the rising Orlando Magic.

Regardless of the success Jackson shared with his team, the tension between Jackson and Bulls general manager Jerry Krause grew. Some believed that Krause felt under-recognized for his work in building the Bulls up into a championship team, being envious of the attention received by Jordan and Jackson. In particular, Krause believed that Jackson was indebted to him because Jackson received his first NBA coaching job from Krause. Some examples of the tension include:

During the summer of 1997, Krause's stepdaughter got married. All of the Bulls assistant coaches and their wives were invited to the wedding, as was Tim Floyd, then the head coach at Iowa State, whom Krause was openly courting as Jackson's successor (and who would eventually succeed Jackson). Jackson and his wife at the time, June, were not even told of the wedding, much less invited, only finding out about the event when the wife of assistant Bill Cartwright asked June what she would be wearing to the reception.[5]

After contentious negotiations between Jackson and the Bulls in that same period, Jackson was signed for the 1997–98 season only. Krause announced the signing in what Chicago media widely considered to be a mean-spirited manner, emphasizing that Jackson would not be rehired even if the Bulls won the 1997–98 title. That triggered an argument between Jackson and Krause in which Jackson essentially told Krause that he seemed to be rooting for the other side and not the Bulls. At that point, Krause told Jackson, "I don't care if it's 82-and-0 this year, you're fucking gone."[5]

Krause publicly portrayed Jackson as a two-faced character who had very little regard for his assistant coaches, a perception that certain Krause associates in the Bulls organization had sought to spread about Jackson. At the height of the hard feelings in the spring of 1998, one of Krause's scouts went to press row in Chicago's United Center to explain to a reporter the insidious nature of Jackson's ego. (excerpt from the Phil Jackson biography Mindgames)

After the Bulls' final title of the Jordan era in 1998, Jackson left the team vowing never to coach again. However, after taking a year off, he decided to give it another chance with the Los Angeles Lakers in 1999.