[4][5] In 2005, the then-owner of the Earthquakes, Anschutz Entertainment Group, announced plans of the team relocating to Houston due to failing efforts to secure a soccer-specific stadium in San Jose.

Playing out of San Jose, the Earthquakes hosted world-class players like George Best on their own roster while receiving visiting star talent like Brazilian football legend, Pele.

At that time, he handed over all existing Hawks player contracts, front-office resources and the rights to play in San Jose State University's Spartan Stadium to MLS in exchange for Type C stock in the league.

The Clash's connections to the Blackhawks continued when the club made the first trade in MLS history, sending Rhett Harty to the MetroStars for Troy Dayak.

One month later, the club made history again, as they hosted the Los Angeles Galaxy in a match that drew 31,728 fans to Spartan Stadium, setting the record for attendance at a sporting event in the city of San Jose.

Prior to reaching the 2003 final, the Earthquakes had rallied from four goals down to beat the Galaxy, 5–4 on aggregate, in a first-round playoff that many MLS watchers described as the greatest in league history.

Following the conclusion of the 2005 season, Earthquakes owner Anschutz Entertainment Group (AEG) were granted permission to potentially move the team if a local buyer could not be found within a 30-day window.

MLS announced that the Earthquakes name, colors, logo, wordmark, history and competitive records would not be transferred, similar to the Cleveland Browns deal in the National Football League, to be used by a future San Jose team.

[12][14] On May 24, 2006, an agreement was reached between Major League Soccer and the principal owners of the Oakland Athletics baseball team, Lewis Wolff and John Fisher, granting them a three-year exclusive option to develop a soccer-specific stadium and bring an expansion franchise to the San Francisco Bay Area.

[18] In 2008, England's Darren Huckerby, the MLS Newcomer of the Year and Ireland's Ronnie O'Brien, who made 28 appearances for the Earthquakes, helped anchor the offense, combining for 10 goals and 10 assists.

The team clinched the Supporter's Shield, its first major trophy since their return to San Jose, and qualified for their first CONCACAF Champion's League tournament as a franchise in 2013.

While the style of scoring late goals were still present in games against New York,[32] Portland[33] and Montreal,[34] the team struggled to find success and quickly found themselves at the bottom of the Western Conference.

[39] Despite a league best record in games played after June,[40] the Quakes failed to qualify for the 2013 playoffs, losing the final spot to Colorado on a goal differential tiebreaker.

[44] Fioranelli made clear early on that he would be prioritizing youth development, international scouting, and generally creating a new identity for San Jose that was younger, more dynamic, and more attacking, intentions which were reflected by his off-season acquisitions of Jahmir Hyka, Florian Jungwirth, Marco Ureña, Harold Cummings, and Danny Hoesen using Targeted Allocation Money.

Illustrating the seriousness of his commitment to improving San Jose, within one week in April Fioranelli made two key additions to the technical staff with the hiring of Alex Covelo as Director of Methodology and Bruno Costa as Head of Scouting.

[48] Fioranelli took his ambitions for San Jose a step further just several days later, when he announced on June 25, 2017, that Dominic Kinnear had been fired, and would be replaced immediately and permanently by Chris Leitch, the club's technical director and former interim general manager.

[53] The team experienced its first loss under Leitch three days later on July 4 at Bobby Dodd Stadium, in a 4–2 loss to Atlanta United FC following red cards to both Kofi Sarkodie and Victor Bernardez; however, this match also saw Tommy Thompson score his first league goal and Chris Wondolowski break Ramiro Corrales' record for career starts at San Jose with his 229th start, as well as tie the league record for most goals scored away at 63.

[54] On July 7, 2017, a multi-year collaboration between the Earthquakes and the German Football Association was announced, "focused on knowledge exchange, game development and machine learning".

[62] San Jose lost in the Open Cup semifinals to Sporting Kansas City, for the second time in franchise history, in sudden death penalties on August 9.

[63] On August 19, Wondolowski became the first player in MLS history to score ten or more goals in eight consecutive seasons, following his successful penalty kick in the dying moments of a 2–2 home draw against the Philadelphia Union, when Shea Salinas was tripped in the box by Joshua Yaro.

[67] San Jose began to make roster moves not long after with contract options being declined for players, most notably for defender Víctor Bernárdez[68] and goalkeeper David Bingham who spent six and seven years with the Earthquakes organization respectively.

Just over a week later, San Jose announced in a joint press conference with their USL affiliate Reno 1868 that they had signed three players from the team: Luis Felipe, Chris Wehan, and Jimmy Ockford.

When they rebranded to the Earthquakes in 2000, the team badge featured an inverted triangular shield containing a soccer ball invoking the rising sun used in the logo for the City of San Jose,[citation needed] a stylized 'Earthquakes' wordmark, and a color palette of blue, black, white and silver.

The jersey release party was held near the site of the USS Hornet Museum and the kit itself presented by a retired SEAL alongside squad members Tommy Thompson, Joel Qwiberg, and, offshore in a military rescue boat, Nick Lima and Jackson Yueill.

The new facility, to have 22,000 permanent seats but be expandable to a capacity of 30,000 for single games, would be privately built by Lewis Wolff and John Fisher, the primary owners of the Earthquakes, with San Jose State providing the needed land.

Additionally, the team and the university would build community soccer fields across Senter Road in Kelley Park using San Jose municipal bond money that had been approved years earlier for the purpose but never spent.

On June 12, 2007, the San Jose City Council voted unanimously to enter into a Memorandum of Understanding to explore construction of a new stadium to bring MLS back to San Jose and adopted a resolution authorizing the city manager to enter into an Exclusive Right to Negotiate agreement with Wolff and his partners regarding the potential development of the former FMC site.

[97] The California Clásico[98][99][100] is a rivalry between two Major League Soccer teams, the LA Galaxy and the San Jose Earthquakes, which existed from 1996 to 2005 and was resumed in 2008.

While there have been several players to play for both teams beforehand, the rivalry intensified after the Anschutz Entertainment Group (owner of the Los Angeles Galaxy) took sole ownership of the San Jose Earthquakes in December 2002.

Along with his band, The Old Firm Casuals, he wrote the new anthem and theme song, "Never Say Die", for the club, which was performed as part of the team's rebranding ceremony on January 30, 2014.