[14][15][16] Throughout organized team activities and training camp, Bouye competed for a roster spot and a job as the fourth cornerback against Brandon Harris, Roc Carmichael, Johnny Adams, and Travis Howard.

[17][18] Head coach Gary Kubiak named Bouye the fifth cornerback on the Texans' depth chart to start the regular season, behind Johnathan Joseph, Kareem Jackson, Brice McCain, and Brandon Harris.

On September 28, 2013, Bouye made his first career tackle on fullback Derrick Coleman during a kick return in the second quarter of a 23–20 loss to the Seattle Seahawks.

[23] During training camp, secondary coach John Butler held an open competition for the job as the third cornerback on the depth chart.

The competition included Bouye, Brandon Harris, Josh Victorian, Elbert Mack, Andre Hal, and Marcus Williams.

[24] Head coach Bill O'Brien named Bouye the third cornerback to start the regular season behind starters Johnathan Joseph and Kareem Jackson.

[25][26] On September 21, 2014, Bouye earned his first career start and recorded three combined tackles in their 30–17 loss at the New York Giants in Week 3, but left in the third quarter after sustaining a groin injury.

[29] In Week 13, Bouye made three solo tackles, a pass deflection, and returned an interception by Jake Locker for a season-long 67-yard gain during the third quarter of a 45–21 victory against the Tennessee Titans.

[31] Throughout training camp, Bouye competed against rookie first round pick Kevin Johnson for the role as the third cornerback on the Texans' depth chart.

[32] Defensive coordinator Romeo Crennel opted to name Bouye the fourth cornerback on the depth chart to start the regular season, behind Johnathan Joseph, Kareem Jackson, and Kevin Johnson.

[37] On January 9, 2016, Bouye appeared in his first career playoff game and recorded a solo tackle in their 30–0 loss to the Kansas City Chiefs in the Wild Card Round.

[38] On March 8, 2016, the Houston Texans signed Bouye to a one-year, $1.67 million tender with a right of first refusal class after he became a restricted free agent in 2016.

[40] He appeared in the Houston Texans' season-opener against the Chicago Bears and recorded three solo tackles, deflected a pass, and his first career sack on quarterback Jay Cutler during their 23–14 victory.

[41] Bouye became the Texans' third cornerback on the depth chart after Kevin Johnson broke his foot the previous week and was sidelined for the remainder of the season.

On October 24, 2016, Bouye started at nickelback and recorded a season-high 11 combined tackles (nine solo) and two pass deflections in the Texans' 27–9 loss at the Denver Broncos.

[44] Bouye had a breakout season in 2016 and finished with a career-high 63 combined tackles (48 solo), 16 pass deflections, an interception, and a sack in 15 games and 11 starts.

He was pursued by many teams, including the Chicago Bears, Jacksonville Jaguars, Tennessee Titans, San Francisco 49ers, Cleveland Browns, Indianapolis Colts, and Philadelphia Eagles.

[53] Head coach Doug Marrone named Bouye the starting cornerback along with Jalen Ramsey entering training camp.

[citation needed] Bouye made his Jaguars' regular-season debut in their season-opener at the Houston Texans and recorded six combined tackles and two pass deflections during their 29–7 victory.

[54] On November 12, 2017, Bouye recorded four combined tackles, broke up a pass, and returned an interception 51-yards to set up Josh Lambo's 30-yard field goal to defeat the Los Angeles Chargers in overtime by a score of 20–17.