The former Manchester United and Chelsea midfielder has joined the club's ownership group.
San Diego's majority owners, the Mansour Group, already have controlling stakes in Danish side Nordsjaelland and the Right to Dream Academy.
In a club announcement confirming his investment, Mata said: "Joining San Diego FC as a partner is an exciting opportunity to help build something truly special in a city and league that are experiencing incredible growth.
"I look forward to contributing my experience and passion for the game and working alongside everyone here to build a club that inspires both on and off the pitch."
Mata has become the first active player to hold an ownership stake in MLS ahead of San Diego joining the Western Conference in 2025.
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The club were founded in May last year and will boast a squad including Mexico's Hirving Lozano and ex-United defender Paddy McNair.
Mata follows in the footsteps of David Beckham, who co-owns this season's Supporters' Shield winners Inter Miami.
However, the former England captain did not become an MLS owner until after his playing career with Beckham becoming co-owner of the franchise in 2021 having retired as a player in 2013.
As for Mata, he also took to X to celebrate his arrival, writing: "Really happy to announce that I'm a partner at the newest and most special franchise in the MLS!
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"Many thanks to the ownership group, @right2dream and @MLS for allowing me to be the first active player to be a part owner of a club in the league, and the second ever after David Beckham. It's truly an honour.
"It's needless to say that the Right to Dream approach to our beloved sport is unique, bringing purpose at the core of everything they do, and I'm really happy to continue my journey using football as a social tool for change together with the Right to Dream community and @CommonGoalOrg.
"I see this step as an opportunity to help build something really special in a city and a league that are experiencing incredible growth, and I cannot wait to be involved and commit to the positive social impact that aligns with the club's and my personal vision of the beautiful game."
San Diego chairman Mohamed Mansour added: "We are absolutely delighted that Juan Mata has joined the club as a partner.
"Juan has been an active and long-term supporter of Right to Dream, and he shares our values of wanting to use football to deliver long-term social impact and change.
"As one of the most successful footballers of his generation, winning the World Cup, European Championship and UEFA Champions League, among many other titles, he is a serial winner, and in San Diego, we are committed to building a winning team for the long term."
Mata's investment in San Diego comes just seven months after he visited the club's 35,000-capacity Snapdragon Stadium.
He toured the arena to promote United's pre-season friendly against Real Betis at the venue and was asked about the facilities and impact of bringing an MLS club to the city.
Back in April, the Spaniard explained: "It's incredible. It's my first time in these facilities and it's incredible there, what they built here.
"The power that it has in society, how they're helping kids with doing sports, any kind of sport."
The 36-year-old won both the World Cup and European Championship with Spain as well as the Champions League during his time at Chelsea.
He is currently playing in Australia for A-League side Western Sydney Wanderers, having signed in September after spells in Turkey and Japan.
Mata now has a stake in San Diego to add to his investment in F1 team Alpine Racing Ltd.