Metropolitan FA was founded in 2012 by
Argentine Jorge Silvetti. By the
2016 season the club was competing in the resurrected Puerto Rico Soccer League, the top tier of football on the island. After finishing in second place during both halves of the regular season, the team had the most combined points in the league and advanced directly to the final. The club won the league championship in the playoff by defeating
Bayamón FC in the final at the
Juan Ramón Loubriel Stadium. As part of pre-season preparations in 2017 Metropolitan FA competed in the annual
Don Bosco Cup. The team won the silver medal in the tournament, falling 0–3 to GPS Puerto Rico in the final. The club finished the abbreviated
2017 regular season in third place before being eliminated in the playoff round. The league ceased operations following the season and Puerto Rico was without a top-tier competition until September 2018. Metropolitan FA joined the nascent
Liga Puerto Rico for its inaugural season in 2018/19. It went on to finish as the first-ever champions of the 8-team league. The club also finished runner-up in the
Copa Luis Villarejo that season. The club began the 2019/20 campaign and was in a close second in the table but the season was eventually abandoned because of the
COVID-19 pandemic and no champion was named. As reigning Puerto Rico champions, the club earned the right to compete in the
2020 Caribbean Club Shield. However, the tournament was also eventually cancelled because of the pandemic. In August 2020 the club announced the signing of all-time leading scorer for the
Puerto Rico national team Hector Ramos. Because no 2020/21 season was held in Puerto Rico, Metropolitan FA was still the nation's reigning champion, thus qualifying the team for an expanded
2021 Caribbean Club Championship which kicked off in May 2021. In preparation for the tournament, the club played two
friendly matches against
San Cristóbal FC of the
Primera División de Republica Dominicana at the
Félix Sánchez Olympic Stadium in March 2021. Metropolitan FA lost the first match 0–3. In the second match, the Puerto Rican side earned a 1–1 draw with Hector Ramos scoring Metropolitan's first-ever goal against an international opponent. Metropolitan opened its
2021 Caribbean Club Championship with a match against
Delfines del Este FC on 15 May. Metropolitan took the lead through a goal by
Jorge Rivera in the 83rd minute but Delfines del Este leveled the score in the fifth minute of stoppage time. The match ended in a 1–1 draw. Two days later, Metropolitan earned its first win in international competition with a 4–0 victory over
Bonaire champions
SV Real Rincon.
Hector Ramos opened the scoring with the eventual game-winner in the sixth minute while
Jorge Rivera scored twice more. Real Rincon had previously won the bronze medal in the
2018 edition of the tournament. On the final matchday of the group stage, Delfines del Este defeated Real Rincon 10–0 and jumped ahead of Metropolitan at the top of the group on goal differential. However,
CONCACAF ruled that Delfines fielded six ineligible players in its match against Metropolitan. As a result, Metropolitan was awarded a win for its match against Delfines, with the Puerto Rican club moving on to the semi-finals as a result. In the semi-final match, Metropolitan and
Inter Moengotapoe of
Suriname played an intense, but scoreless first half. Inter Moengotapoe broke the deadlock in the 53rd minute and went on to win 3–1 with Metropolitan's goal coming from Marc Nieves in the 95th minute. By advancing the semi-finals, Metropolitan FA secured a place in the preliminary round of the
2021 CONCACAF League, On 16 June 2021 it was determined by draw that Metropolitan FA would face
FC Santa Lucía Cotzumalguapa of
Guatemala in the
Preliminary Round. In preparation for the series, the club signed former French youth international
Jordan Barbara and Puerto Rican striker
Ricardo Rivera. ==Stadium==