Instead, on June 8, 2021, the NWSL announced San Diego as the location for an expansion team owned by Burkle to begin play in 2022.

After defeating the Chicago Red Stars 2–1,[7] the team traveled to Providence Park to play against the Portland Thorns in the semi-finals, losing 2-1 following a Crystal Dunn goal in the final minutes of the game.

[9] In the 2023 season, the Wave continued their winning ways, slightly improving upon their record in 2022 and securing the NWSL Shield with two games to spare after beating the Portland Thorns on September 30 and guaranteeing a bye for the playoffs.

Defender Naomi Girma was named U.S. Soccer's Female Player of the Year, recognizing her excellence for the Wave and for the U.S. women's national team.

On March 14, owner Ron Burkle announced the sale of San Diego Wave FC to Lauren Leichtman and Arthur Levine, managers of the Levine Leichtman Capital Partners investment firm, for $113 million and a total (and, at the time, league record) team valuation of $120 million.

[20] In July, several former Wave employees spoke out on social media, alleging that the club and president Jill Ellis created an unhealthy and abusive work environment.

[21][22] In mid-October, five former employees filed a lawsuit against the Wave and the NWSL, alleging discrimination, sexual harassment, wrongful termination, and retaliation.

[25] On January 7, 2025, Swedish manager Jonas Eidevall was announced to be filling the role, becoming the Wave's second-ever full-time head coach in club history.

It moved to Snapdragon Stadium, located in the Mission Valley campus expansion of San Diego State University (SDSU), for its last two home games of the 2022 season.