After being named the 2013 PFWA Defensive Rookie of the Year with the Bills, Alonso missed his second season due to a torn anterior cruciate ligament (ACL) and was then traded to the Philadelphia Eagles in 2015.

He also tallied double figures in tackles in 10 of 12 games, finished third on the team in quarterback sacks, and led the Wildcats in receiving (35 catches, 559 yards).

He led Central Coast's sixth-ranked team to the league title (10–1–1) in 2007, with its lone loss his final year coming against Gilroy (40–34) in the sectional semifinals.

[4] He returned the following season and was Oregon's eighth-leading tackler ranked fourth among linebackers with 46 stops, including 6 tackles for loss and 2.5 sacks.

[9] He was re-instated to the Ducks football team in early September 2011 after completing over community service and an alcoholic awareness program.

[18][19] He made his professional regular season debut and first career start in the Buffalo Bills' season-opener against the New England Patriots and recorded nine combined tackles during their 23–21 loss.

Alonso intercepted a pass by Panthers' quarterback Cam Newton, that was originally intended for fullback Mike Tolbert, during the first quarter.

Alonso started in all 16 games as a rookie in 2013 and recorded 159 combined tackles, four interceptions, four pass deflections, two sacks, and one forced fumble.

[30] Bills General Manager Doug Whaley announced that Alonso would be shifted to the weakside linebacker position for the 2014–15 NFL season.

[31] Shortly after however, Alonso tore his anterior cruciate ligament while working out in Oregon and missed the entire 2014 season, as a seven to nine-month recovery was expected.

[34] On March 10, 2015, the Buffalo Bills traded Alonso to the Philadelphia Eagles in exchange for running back LeSean McCoy.

[36] Head coach Chip Kelly named Alonso a backup inside linebacker to begin the regular season, behind DeMeco Ryans and Mychal Kendricks.

[37] During the second quarter of a Week 2 contest against the Dallas Cowboys on September 20, 2015, Alonso suffered a Grade II sprain – a partial tear – of his repaired left anterior cruciate ligament.

Head coach Adam Gase named Alonso the starting middle linebacker to begin the regular season, alongside Koa Misi and Jelani Jenkins.

On November 13, 2016, Alonso made four solo tackles, broke up a pass, and returned an interception for his first career touchdown during a 31–24 win at the San Diego Chargers in Week 10.

Alonso intercepted a pass by Chargers' quarterback Philip Rivers, that was intended for wide receiver Tyrell Williams, and returned it for a 60-yard touchdown during the fourth quarter.

[42] Alonso finished his first season as a member of the Miami Dolphins with 115 combined tackles (69 solo), four pass deflections, two interceptions, and one touchdown in 15 games and 15 starts.

Head coach Adam Gase named Alonso the starting weakside linebacker to begin the regular season.

He received a personal foul penalty and subsequent fine after colliding with a sliding Andrew Luck during a week 12 loss to the Indianapolis Colts.

[58] On November 2, 2020, Alonso was traded to the San Francisco 49ers with a conditional fifth-round pick in the 2021 NFL draft in exchange for LB Kwon Alexander.

[59] Alonso was eligible to practice with the Saints and 49ers since October 19, 2020, but the 49ers declined to activate him from the PUP list by November 14, 2020, and he was ineligible to return during the season.