Saunders then moved to the La Crosse (Wisconsin) Catbirds for five seasons (1989-94), where he won two CBA Championships, before coaching in 1994-95 with the Sioux Falls Skyforce. He also served as general manager (1991-93) and team president (1991-94) of the Catbirds. Saunders' impressive CBA tenure included seven consecutive seasons of 30 or more victories, two CBA championships (1990, 1992), two CBA Coach of the Year honors (1989, 1992) and 23 CBA-to-NBA player promotions.
This happened shortly after McHale took over basketball operations for the Timberwolves. He added the coaching duties to his GM responsibilities after the team got off to a 6-14 start. The Timberwolves went 20-42 the rest of the year, but the emergence of young Kevin Garnett as a front-line NBA player was a major plus over the second half of the season.
He guided the Timberwolves to their first-ever playoff berth in the 1996-97 season, his first full season as an NBA head coach, and to a franchise-record 50 victories in 1999-2000 which was duplicated in 2001-2002.
After the Timberwolves' success in the 2003-04 NBA season, in which they made the Western Conference Finals, they struggled in the 2004-05 season, winning fewer than half of their games. On February 12, 2005, Saunders was fired and replace by then-Vice President of Basketball Operations Kevin McHale as head coach. Many fans believed that the firing was unwarranted, citing instead the contract troubles of Sam Cassell and Latrell Sprewell as the reasons for the team's failure. However, many also acknowledged that Saunders had already coached eight seasons in Minnesota, and perhaps a new voice was needed.
Despite the successful season, however, Saunders has been a target of criticism for the Pistons' playoff performance, in which the Cleveland Cavaliers pushed them to 7 games in the 2006 Eastern Conference Semifinals. The worn-out Pistons then lost the Eastern Conference Finals to the Miami Heat in 6 games. Saunders has received criticism for the poor defensive showing by the Pistons in the East finals. This has been speculated as a deciding factor in Ben Wallace's decision to sign a free-agent contract with the rival Chicago Bulls in the 2006 offseason. The 2007 playoffs also ended in disappointment for Saunders and the Pistons as the Cavaliers rallied from a 2-0 deficit to win the next four games and the Eastern Conference title.
Upon entering his third season as Pistons coach, Saunders became the longest-tenured Pistons coach since Chuck Daly's nine-year tenure (1983-1992).
Saunders was fired June 3 2008 after the Pistons lost to the Boston Celtics in the 2008 Eastern Conference Finals; Detroit president of basketball operations Joe Dumars said the team needed a "new voice".
In 2005-06, Flip became the head coach of the Detroit Pistons following the complex departure of Larry Brown, who left to coach the New York Knicks. The Pistons were coming off back-to-back NBA Finals appearances including one NBA Championship in 2004. The Pistons had the NBA's best record in 2006, had four All-Stars in their starting lineup, and were the heavy favorite going into the playoffs to capture the NBA Championship. However, they lost the Eastern Conference Finals to the Miami Heat, 4 games to 2.
The Pistons lost Ben Wallace in the off-season to the Chicago Bulls, but added playoff veteran Chris Webber, who came to Detroit out of his desire to win a championship. In the 2006-07 season, the Pistons had the best record in the Eastern Conference, but lost in the Eastern Conference Finals 4-2 to LeBron James and the Cleveland Cavaliers. In the 2007-2008 season, the Pistons finished with the second-best record in the league, but lost to the Boston Celtics in the Eastern Conference Finals, 4-2. Saunders is known as an offensive guru, and because of this he was not welcomed in Detroit. His defensive schemes as a coach came into question, and thus his tenure as Pistons head coach was very much scrutinized.
|- | align="left" |MIN | align="left" |1995–96 |62||20||42||.323|| align="center" |6th in Midwest||—||—||— | align="center" |Missed Playoffs |- | align="left" |MIN | align="left" |1996–97 |82||40||42||.488|| align="center" |3rd in Midwest||3||0||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |1997–98 |82||45||37||.549|| align="center" |3rd in Midwest||5||2||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |1998–99 |50||25||25||.500|| align="center" |4th in Midwest||4||1||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |1999–00 |82||50||32||.610|| align="center" |3rd in Midwest||4||1||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |2000–01 |82||47||35||.573|| align="center" |4th in Midwest||4||1||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |2001–02 |82||50||32||.610|| align="center" |3rd in Midwest||3||0||3 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |2002–03 |82||51||31||.622|| align="center" |3rd in Midwest||6||2||4 | align="center" |Lost in First Round |- | align="left" |MIN | align="left" |2003–04 |82||58||24||.707|| align="center" |1st in Midwest||18||10||8 | align="center" |Lost in Conf. Finals |- | align="left" |MIN | align="left" |2004–05 |51||25||26||.490|| align="center" |(fired)||—||—||— | align="center" |— |- | align="left" |DET | align="left" |2005–06 |82||64||18||.780|| align="center" |1st in Central||18||10||8 | align="center" |Lost in Conf. Finals |- | align="left" |DET | align="left" |2006–07 |82||53||29||.649|| align="center" |1st in Central||16||10||6 | align="center" |Lost in Conf. Finals |- | align="left" |DET | align="left" |2007–08 |82||59||23||.720|| align="center" |1st in Central||17||10||7 | align="center" |Lost in Conf. Finals |- | align="left" |Career | ||983||587||396||.597|| ||98||47||51 |}