After junior college, John chose to finish his college career at Portland State University, where he broke the single-game yardage mark by throwing for 592 yards and 8 touchdowns in 3 quarters against Cal Poly, after he took over in the 5th game of the season. He finished the season ranked second in passing efficiency with 61 percent, 201 of 331 for 3,527 yards, and 41 touchdowns and only 11 interceptions.
As a senior, he led the nation in total offense averaging 338 yards, completed 194 of 281 for a school-record 69 percent, 2944 yards, 24 touchdowns, and only 8 interceptions to rank second in the nation in passing efficiency with a 181.3 rating for the second straight season. For which, he was named Western Conference best player two years consecutively.
John was the first player in Western Conference history to be named player of the week four times in one season, three weeks in a row, seven times in two seasons.
He was named Sports Illustrated national player of the week in 1991, named national player of the week twice in 1992 with USA Today and Sports Illustrated, honored by NCAA for winning total offense national title in 1992, passed for three touchdowns or more in 17 of 18 starts the past two seasons, three or more touchdowns in every game.
He was also an Oregon Banquet of Champions finalist two years in a row, finalist for the prestigious Harlon Hill Award (Division II’s equivalent of the Heisman Trophy).
Despite wrist injury and 8 games, he finished third in balloting with 106 points and 13 first place votes. He completed a perfect sweep of NCAA All-America First Teams by being selected to the USA Today All-America Team, Kodak/American Football Coaches Association, and the Associated Press All-America Teams.
He was one of five National Jefferson Award winners for Public Service in 1993. Winners receive a Bronze medallion from the Franklin Mint in Washington, D.C. and also published with the American Institute for Public Service in Washington, D.C.