Woodruff returned to the UW staff in 1984 as quarterbacks coach as the Huskies won the Orange Bowl; the undefeated 1991 team won a second consecutive Rose Bowl and shared the national title.
He succeeded Keith Gilbertson as the Huskies' offensive coordinator in 1992 under James and continued in 1993 under new head coach Jim Lambright.
After leaving the Washington program in January 1994, Woodruff moved to Arizona and was the head coach at Cholla High School in Tucson, then joined the University of Arizona staff as an assistant in 1998 under head coach Dick Tomey.
[1] Woodruff was hired as head coach at Eastern Michigan University in 2000 and compiled a 9–34 (.209) record in four seasons.
Following a 38–10 loss to Central Michigan in 2003 on November 1, athletic director Dave Diles, Jr. fired Woodruff and stated, "Jeff Woodruff has helped develop our program with quality young men, but the team is not on the competitive level that we felt should be after four years.