The club was established on February 21, 2021,[2] and is a member of the USL Championship, the second tier of the American soccer league system.

[7] The 2007 NPSL season would see two Monterey Bay teams playing in the same league, with the Santa Cruz County Breakers established.

The team, owned by Ray Beshoff, ceased operations after the 2019 season because he was unable to secure construction of a soccer-specific stadium.

[11][12] In April 2021, former San Jose Earthquakes captain, Ramiro Corrales, joined the team staff as a technical advisor.

[18] Due to the timing of the renovation of Cardinale Stadium, the team started the regular season with seven consecutive league road matches.

[19] The club's first ever professional win occurred on March 26, 2022, in their third ever match, away to nearby Northern California side Oakland Roots SC.

[21] The club had their first ever home match on May 7, 2022, defeating Las Vegas Lights FC 1–0 on a goal by Walmer Martinez in the 56th minute.

[25][26] Newcomer Alex Dixon scored the club's first ever hat trick in the 2023 USL Championship season opener against Hartford Athletic.

[30] The club would once again host MLS competition in the US Open Cup, but this time they fell in a penalty-shootout against Los Angeles FC.

The program would identify young talent in the Monterey, Santa Cruz, and San Benito tri-county area and allow them to train at the club's facilities and with their staff throughout the year.

[35] Three Monterey Bay FC 2 players were added to the roster ahead of the 2024 USL Championship season: Pierce Gallaway, Miguel Guerrero, and Anthony Orendain.

[48] The club's initial open tryouts saw 85% of the players either currently based in or originally from Monterey County, with the largest amount of registrants coming from Salinas.

CSUMB student José Jesús Madrigal scored the club's first goal in what ended as a 1–1 draw at Rabobank Stadium.

[56] On October 28, 2023, Monterey Bay FC Principal Owner Ray Beshoff stated that one of the club's goals is to develop MBFC2 into a year-round program.

[36] On March 13, 2024, two more MBFC2 players, Miguel Guerrero and Anthony Orendain, were added to the first team's roster ahead of the 2024 USL Championship season.

[58] Ahead of the team's second season, Monterey Bay player Simon Dawkins took over as head coach from Ramiro Corrales.

[59] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.