In 1988-89 Jordan turned in possibly the best all-around performance of his career. The league's leading scorer once again at 32.5 points per game, he finished 10th in the NBA in assists with a career-high 8.0 per outing and also set a career high by pulling down 8.0 rebounds per contest. He ranked third in the league in steals at 2.89 per game. On January 25 he scored the 10,000th point of his career. Named to the East All-Star Team for the fifth straight year, Jordan scored 28 points in 33 minutes of action. His postseason honors included membership on the All-NBA First Team and the NBA All-Defensive First Team and selection as Player of the Year by The Sporting News.

The Bulls slipped a bit in the regular season, posting a 47-35 record, 3 fewer wins than the season before. But after squeezing by the Cleveland Cavaliers in five games in the opening round of the playoffs, the Bulls ousted the New York Knicks in the conference semifinals and advanced to the Eastern Conference Finals for only the third time in team history. They fell to the Detroit Pistons in six games. Jordan averaged 34.8 points in 17 postseason games. In the pivotal Game 5 of Chicago's first-round series against Cleveland, Jordan hit a memorable buzzer-beating jumper over Craig Ehlo to bring the Bulls from a 100-99 deficit to a 101-100 victory.

Phil Jackson took over as head coach of the Bulls for the 1989-90 season, and everything started to click for Chicago. The Bulls put together a 55-27 record, the club's best showing since it had gone 57-24 under Dick Motta in 1971-72. Jordan was his usual dominating self at both ends of the court, leading the NBA in scoring (33.6 ppg) and steals (2.77 per game). He set a personal best when he scored 69 points in a 117-113 overtime win against the Cleveland Cavaliers.

He also emerged as a legitimate threat from beyond the three-point arc, posting a .376 percentage-100 percentage points above his previous career high-while hitting 92 long-range shots, compared with 68 in his first five seasons combined. A member of the All-Star Team once again, Jordan was also picked for the All-NBA First Team and the NBA All-Defensive First Team. In the postseason the Bulls got past the Milwaukee Bucks and the Philadelphia 76ers in the first two rounds but fell to the Detroit Pistons in seven games in the Eastern Conference Finals. Jordan averaged 36.7 points in 16 playoff games.