Allen had a breakout season in 2020 when he led the Bills to their first division title and playoff victory since 1995 en route to an AFC Championship Game appearance.

San Diego State made him an offer to walk on, but Allen turned it down because Aztecs coach Rocky Long could not guarantee any playing time.

They spurned overtures from more prominent Central Valley programs after Allen's breakout junior season and kept him at Firebaugh, living by the family mantra that "you bloom where you're planted."

Not only was Allen involved in multiple sports while in high school, he also regularly worked on the family farm and at the restaurant his mother operated in Firebaugh.

He received numerous awards for his agricultural work and knowledge including a rank in the top four in the nation in diversified crop production of cantaloupe, cotton, and wheat in 2014.

Bohl was the only FBS head coach to visit the family farm, and while there, he told Allen's father, "We went all around the country and there's only one quarterback we want and that's your son.

"[2] In December 2017, after leading the 8–5 Cowboys to a 37–14 win over Central Michigan in the 2017 Famous Idaho Potato Bowl, Allen announced he would be entering the 2018 NFL draft.

[55] Despite being placed in the concussion protocol, Allen returned the following week against the Titans, completing 23 of 32 pass attempts for 219 yards, two touchdowns, and one interception in a 14–7 Bills win.

[61] In Week 16, in a rematch against the Patriots, Allen passed for 208 yards and two touchdowns, including a 53-yarder to John Brown, but Buffalo fell short once again, losing 24–17 to surrender the division title to New England.

[68] In the AFC Wild Card Round against the Texans, Allen started strong, breaking Jim Kelly's franchise post-season record for rushing yards by a quarterback (37) with a single 42-yard run on the first drive,[69] and caught a 16-yard touchdown pass from wide receiver John Brown on a trick play, similar to what Nick Foles did in Super Bowl LII.

[122] Against the Atlanta Falcons in Week 17, Allen threw for a career-high three interceptions and had a career-low passer rating of 17, but rushed for 81 yards and two touchdowns on the ground as Buffalo relied on its running game to win 29–15 and clinched its fourth playoff berth in five seasons.

The Chiefs won 42–36 in the extra period after winning the coin toss and scoring on the opening drive as Allen and the Bills offense never touched the ball.

[141] Following the bye week, Allen threw for 218 yards, two touchdown passes, and two interceptions in a 27–17 victory against the Green Bay Packers on Sunday Night Football.

[148] Against Detroit on Thanksgiving Day, Allen led the Bills to a comeback win with a strong fourth quarter performance, including a touchdown to retake the lead and a 36-yard pass to Stefon Diggs that helped set up the game-winning field goal.

Allen would then lead Buffalo on a 7-play drive, that included a season-long 44-yard run, and was capped off by a Dawson Knox touchdown catch and a successful two-point conversion to tie the game at 29–29.

[160] In Week 4 against the Dolphins, Allen achieved a perfect passer rating of 158.3 for the first time in his career, completing 21 of 25 passes for 320 yards and 4 touchdowns while rushing for another score on the ground, as the Bills won 48–20.

[161][162] However, following this game, Allen and the Bills offense entered a six-game stretch characterized by inconsistency, crucial turnovers, and a general lack of scoring until the second half, with losses to the Jaguars,[163] Patriots,[164] Bengals,[165] and Broncos.

[166] When asked about the team's struggles during this stretch, Allen stated that he was attempting a "low positive" mentality on the field in contrast to his typically fiery and emotional playing style and pondered if he had "reined himself in too much".

[167] Under Brady, Allen and the Bills won six of their final seven games with a more balanced attack on offense, winning their fourth consecutive division title after beating Miami 21–14 in Week 18.

To offset the departures of Diggs and Davis, the Bills replaced them with veteran free-agent receivers such as Curtis Samuel, Mack Hollins, and Marquez Valdes-Scantling while drafting Keon Coleman, with Joe Brady insisting on an "everybody eats" mentality among the offense rather than focusing on a singular player.

However, following the 3–0 start, Allen struggled in losses against the Baltimore Ravens and Houston Texans in which he suffered two big hits that caused him to be attended by the medical staff, namely a failed flea flicker against Baltimore that arguably stalled the Bills' comeback efforts,[178] and a hit against Houston in which spectators opined he had suffered a concussion due to Allen's head "violently" bouncing off the ground after he landed on his ankle and chest, but he was deemed fine and allowed to finish the game after missing just under five minutes and given smelling salts.

[184] The following week, in a 44–42 loss to the Los Angeles Rams, Allen tallied 424 total yards and became the first player with three passing and three rushing touchdowns in a regular season game.

[192][193] At home in the Divisional Round against the Baltimore Ravens, Allen threw for just 127 yards, but also ran for two touchdowns in a close 27–25 win en route to the AFC Championship.

[195] Allen has received praise for his unique combination of size, arm strength, speed, running ability, and overall athleticism, drawing comparisons to John Elway,[236] Randall Cunningham,[237] Brett Favre,[238] and Cam Newton.

[239] However, his work ethic and training under former offensive coordinators Brian Daboll and Ken Dorsey, in addition to throwing coaches Jordan Palmer and Chris Hess, have been cited as instrumental in his development into a more accurate and methodical passer.

His pregame playlist includes entries by Frank Sinatra ("That's Life"), Sammy Davis Jr., Elvis Presley, Paul Anka ("Put Your Head on My Shoulder"), and Billy Joel ("The Stranger").

He stated in 2023 that "I haven’t been the most devoted Christ-follower in my life, and I’ve had my different beliefs and thoughts and ideas and stuff like that," but that he had seen enough evidence of divine intervention to believe "God's real.

[262] Allen worked with New Era's creative team to design a special-edition cap released and sold in October 2019 to benefit Oishei Children's Hospital in Buffalo.

[263] Following in Jim Kelly and Doug Flutie's footsteps, Allen partnered with PLB Sports & Entertainment and Wegmans in 2020 to produce his own cereal, Josh's Jaqs.

[270] Allen has a personal connection to children's health because his younger brother, Jason, was hospitalized for a few days as a child with Kawasaki disease, a rare condition which inflames blood vessels.