He left Pittsburgh to become the Panthers head coach in 1995, where he guided the team to a 7–9 record, the best finish for an NFL expansion franchise's inaugural season.

The next year, Capers led the Panthers to a division title and the NFC Championship Game, making them the youngest NFL expansion franchise to accomplish both.

Capers' early success with Carolina would result in him serving as the inaugural head coach of the Texans from 2002 to 2005, although he was unable to lead them to a winning record or playoff berth.

He continued to hold assistant coaching positions afterwards, most prominently as the defensive coordinator of the Green Bay Packers from 2009 to 2017, who he helped win Super Bowl XLV.

After a stint in the USFL, he began his NFL career as an assistant with the New Orleans Saints and was named defensive coordinator of the Pittsburgh Steelers in 1992, including a trip to the AFC Championship game in 1994.

Continuing to spend against the salary cap, and eventually taking control of personnel matters in 1997, the Panthers went 7–9, followed by a 4–12 season in 1998, at the end of which he was terminated.

After being let go from the Panthers, he served as the defensive coordinator with the Jacksonville Jaguars until becoming the head coach of the expansion Houston Texans on January 21, 2001.

[11] Following a year-long stint with the Broncos, Capers returned to the Carolina Panthers to serve as a senior defensive assistant under newly hired head coach Frank Reich.