2010s īetween 20, the chain closed stores in Berkeley, Pasadena and Torrance, California. In 2009, Baja Fresh moved its corporate headquarters from Thousand Oaks to Cypress, California, and closed all locations in central Ohio.

The consortium was led by David Kim, who took on the role of CEO, and later appeared on Season 2 episode 20 of the reality TV series Undercover Boss. At the time of the firm's acquisition by BF Acquisition Holdings in 2006, Baja Fresh had 144 company-owned and 154 franchised locations in the states of Arizona, California, Colorado, Connecticut, Florida, Idaho, Illinois, Indiana, Maryland, Massachusetts, Michigan, Nevada, New Jersey, New York, Ohio, Oregon, Pennsylvania, Tennessee, Texas, Virginia, Washington as well as the District of Columbia. In 2006, Wendy's sold the roughly 300-location Baja Fresh chain for $31 million to BF Acquisition Holdings, a private investor consortium that had operated franchised restaurant units for such chains as Sweet Factory, Cinnabon and Denny's. As a wholly owned subsidiary of Wendy's, the 249 restaurant chain saw consistently declining same-store sales. In 2002, Wendy's International purchased Baja Fresh for $275 million. Dollarhyde became CEO with Siracusa as Chairman and Magglos as President, they then grew the chain from 45 locations in 1998 to 249 stores. In 1998, the Magglos worked with Greg Dollarhyde and Pete Siracusa, who recapitalized the parent company, acquired venture capital and bought shares from outside holders to take control of Baja Fresh. Franchising began in 1995, and the chain had expanded to 31 outlets by 1997.

In 1990, Jim and Linda Magglos took out a third mortgage on their home and opened the first Baja Fresh in Newbury Park, California in the Conejo Valley. A Baja Fresh restaurant on Sunset Boulevard in Hollywood, California, in 2008 1990s

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