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Former Monterey Bay teams

The Monterey Bay area had its first professional team in 1993 when Santa Cruz Surf joined the USISL. The team would only last through the 1994 season, but professional soccer's absence would not last long as the Monterey Bay Jaguars were established for the 1995 season. The following season the Jaguars would change the location in their name to "California" and have their most successful season, defeating the Richmond Kickers 2-1 to win the USISL Select League Championship. The Jaguars would continue to play in USL affiliated leagues until their folding after the 1999 USL D3 Pro League season.

National club soccer would not return to the Monterey Bay until 2004, when the Salinas Valley Samba joined the Men's Premier Soccer League for its second season. The 2007 NPSL season would see two Monterey Bay teams playing in the same league, with the Santa Cruz County Breakers established. However this would not last long, as the Breakers would fold their NPSL club in 2008. The Samba themselves would fold the following year, with the 2009 season being their last. In 2018, a decade after the initial Breakers team folded, the club reestablished their first-team side and joined the USL PDL under the name Santa Cruz Breakers FC.

From Fresno to the Monterey Bay

Monterey Bay F.C. is a continuation of the USL Championship's former Fresno FC franchise. The team, owned by Ray Beshoff, ceased operations after the 2019 season because he was unable to secure construction of a soccer-specific stadium. Beshoff retained franchise rights and sought another place in California to relocate. On February 1, 2021, Monterey Bay F.C. joined the USL Championship. The club's Sporting Director is two-time MLS Coach of the Year, Frank Yallop. Yallop had previously served as general manager of Fresno FC. In April 2021, former San Jose Earthquakes captain, Ramiro Corrales, joined the team staff as a technical advisor. Corrales, a native of Salinas, began and ended his playing career in the Monterey Bay Area. His career began with the Monterey Bay Jaguars in 1995 before joining the San Jose Clash (later renamed "Earthquakes") in 1996. He last served as a player-coach with Santa Cruz Breakers during the 2018 USL PDL season. General manager Frank Yallop was also named head coach on April 22, 2021, with Ramiro Corrales as assistant coach.

First USL Championship seasons

The club announced their first signing, Walmer Martinez, on December 22, 2021. Born in Santa Cruz, Martinez had previously played with fellow USL Championship side Hartford Athletic but was brought in by Monterey Bay, through a transfer for an undisclosed fee, to play professionally at the same campus he had featured collegiately with CSUMB. The club's ever first match was a pre-season encounter away to MLS club San Jose Earthquakes. Monterey Bay ended up losing the encounter 4–2. The club's final signing before the season started was another local product and CSUMB alum, Adrian Rebollar. Rebollar, a native of Watsonville, was a trialist during the preseason and made it to the first team. Due to the timing of the renovation of Cardinale Stadium, the team started the regular season with seven consecutive league road matches. 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. Club captain Hugh Roberts scored the winning goal of the 2–3 victory in the final minute of regulation. Another away match was added to their schedule for their US Open Cup debut, an away match against NISA club Bay Cities FC. Monterey Bay ultimately suffered an upset, losing 2–1 against the 3rd division side. 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. After a late playoff push, the Union ultimately finished their inaugural season in 12th place, second to last in the Western Conference and seven points away from qualifying for the playoffs.

In preparation for their second season, Monterey Bay brought back 17 players from their inaugural squad. Newcomer Alex Dixon scored the club's first ever hat trick in the 2023 USL Championship season opener against Hartford Athletic. The hat trick's first goal featured the fastest goal in club history (91 seconds) and the third goal was the first penalty scored by the club. His performance also earned him USL Championship Player of the Week honors, another first for a player from the club. The club won their first ever U.S. Open Cup match on April 5, 2023, away to Central Valley Fuego FC, the club which filled the professional soccer void in Fresno after Fresno FC folded to eventually become Monterey Bay FC itself. In the following round Monterey Bay achieved their most important win in club history, upsetting local MLS club San Jose Earthquakes 1–0. It was their first competitive match against a first division club in their history. 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 match against LAFC featured the club's highest ever attendance, just shy of a sellout with 5,808 fans on hand. Despite a hot start to the season, Monterey Bay would ultimately finish the season in 11th place, once again 2nd to last in the Western Conference and six points away from qualifying for the playoffs.

Following the 2023 season, Monterey Bay FC Principal Owner Ray Beshoff stated that the club's goals for the offseason were to broaden their developmental side Monterey Bay FC 2 into a year-round program as well as to expand their academy's development to reach more youth in the community. The club announced their initial roster decisions ahead of the 2024 season on November 28, 2023. The most notable departures were the club's first captain Hugh Roberts as well as the club's all-time leading goal scorer Christian Volesky. The club announced a U-18 Development Academy on February 5, 2024. 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. 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.