Bayamón

1999–2005

Bayamón FC was formed in 1999. They began to play in the Liga Mayor de Fútbol Nacional. They were very successful during their period in the league, becoming champions in the years 2000 and 2002, second place in 2003 and third place in 2004.

2009 season

Bayamón FC played in the first game of the 2009 Puerto Rico Soccer League season against defending champions Sevilla FC, which Sevilla FC won 1–0. Bayamón then defeated Humacao Tornados 8–1 and Guaynabo Fluminense 4–1. After finishing second in the league table, Bayamón captured the playoff championship with a 3–2 aggregate victory over Atléticos de San Juan.

2010–2013

The team did not participate in the Puerto Rico Soccer League for the 2010 and 2011 seasons due to the league's instability. PRSL eventually folded after the 2011 Supercopa tournament. Instead, they played in the Liga Nacional de Fútbol de Puerto Rico, and they were champions during the 2010 and 2011 seasons.

2014 season

The team was renamed Puerto Rico BFC and was expected to play in the National Premier Soccer League. In the end the team never played in the league, but still qualified to the CONCACAF Champions League by winning their matches in the 2014 CFU Club Championship. Francisco Arias was their head coach during the 2014 season.

2016: Partnering with David Villa

In January 2016, it was announced that Bayamón FC would join legendary Spanish striker David Villa on his new project of building soccer academies worldwide. Bayamón FC became the first academy from the DV7 program.

Delfín Ferreres joined the coaching staff of the Bayamón FC senior team during the PRSL Clausura 2016 Tournament, which they won.

2017 season

Bayamon snatched up former Quintana Academy captain Luis Bermudes following the teams decision not to participate in the first division in 2017.

2018–19 season

Following the exit of Delfín Ferreres, Marco Vélez was appointed Head Coach for the 2018 season. Bayamón hosted their annual Bayamón Cup, losing in the finals on penalty shootout against Blazers FC.

From March 2018, they played in the Puerto Rican Football Federation Preparatory Tournament. With a dominant winning streak, Bayamón secured their spot in the semi-finals stage. Bayamón won the title after winning 1–0 against GPS Puerto Rico.

In August 2018, it was announced that Bayamón FC will participate in the inaugural season of the Liga Puerto Rico. Spanish coach Josep Ferré took charge of the team in September 2018.

Bayamón FC finished runners-up in the Liga Puerto Rico after losing the final in penalty shootout against Metropolitan FA. However they ended up winning the second edition of the Copa Luis Villarejo defeating Metropolitan FA 4-2 in the final.

2019-20 season

In July 2019, it was announced that Delfí Ferreres will take charge of the team.

2021-present

In March 2021, it was announced that Bayamón FC agreed to a professional partnership with newly formed USL Championship team Queensboro FC.

In December 2021, Bayamón FC became champions of the 2021 Liga Puerto Rico after defeating Metropolitan FA 1-2 in the final match played at the Mayagüez Athletics Stadium.