Baldwin was the head football coach at Cal State Northridge from 1995 to 1996, compiling a record of 9–12. He was also the head football coach at San Jose State.
During his tenure as head coach at San Jose State from 1997 to 2000, he had three straight wins over Stanford (including in their Rose Bowl season of 1999). In 1997, SJSU upset No. 24 Air Force, (25–22) their first win over a ranked opponent since 1990. In 2000, SJSU beat ninth-ranked TCU (27–24) ending their 12-game winning streak. Also in 2000, SJSU earned a mark of 7–5, their first winning season in eight years. His overall record at San Jose State University was 18–27.
In 2015, Baldwin joined Oregon State as offensive coordinator and tight ends coach under Gary Andersen. The following season, Baldwin left his duties as offensive coordinator and became the inside receivers coach. He later became tight ends coach in 2017.[2] Baldwin and other assistant coaches were fired on November 26, 2017 as Oregon State continued its coaching search, over a month after Andersen resigned and Cory Hall took over as interim head coach.[3]