1990s

In 1990 Jim and Linda Magglos took out a third mortgage on their home^[3] and opened the first Baja Fresh in Newbury Park, California in the Conejo Valley. Franchising began in 1995,^[3] and the chain had expanded to 31 outlets by 1997.^[4] 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.^[3][5] Dollarhyde became CEO with Siracusa as Chairman and Magglos as President, they then grew the chain from 45 locations in 1998 to 249 stores.^[6]

2000s

In 2002, Wendy's International purchased Baja Fresh for $275 million.^[7] As a wholly owned subsidiary of Wendy's, the 249 restaurant chain^[8] saw consistently declining same-store sales.^[8] 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.^[9] 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.^[10] The consortium was led by David Kim, who took on the role of CEO,^[8] and later appeared on Season 2 episode 20 of the reality TV series Undercover Boss.^[11]

In 2009, Baja Fresh moved its corporate headquarters from Thousand Oaks to Cypress, California,^[4] and closed all locations in central Ohio.^[12]

2010s

Between 2009 and 2010, the chain closed stores in Berkeley, Pasadena and Torrance, California. When the chain opened its first international location in Dubai in 2010, the chain also had 255 restaurants in 28 U.S. states.^[13]

In late 2011, the company moved its main corporate office from Cypress to Irvine. In early 2012, the chain closed its store in Newbury Park, California, although this was a different location in Newbury Park than the original site of the first Baja Fresh.^[14] On April 12, 2013 Baja Fresh closed all five locations in Phoenix, Arizona, without notice.^[15]

On April 5, 2012, David Kim stepped down from his position as company CEO. His position was assumed by company president Chuck Rink, who began to hold both titles.^[16]

Five Phoenix-area locations were closed by a franchise operator in 2013.^[17]

In September 2016, it was announced that Baja Fresh's parent, BF Acquisition Holdings, was sold to MTY Food Group for $27 million.^[1] At the time of the acquisition by MTY, Baja Fresh had 162 restaurants and its sister company La Salsa had 23 restaurant with 16 of the combined 185 locations were franchised.^[1] It is unclear if the new owner would combine the two chains or keep them separate. In an earlier press release announcing MTY's acquisition of Kahala Brands just two months previously, MTY gave the vague statement that "Kahala will stay in Kahala's current headquarters... while MTY's US operations will move into Kahala's offices".^[18] This statement could imply that Baja Fresh might become a subsidiary of Kahala instead of just sharing space with Kahala and reporting directly to MTY corporate headquarters in Canada. Published newspaper reports are not very clear about the exact relationship between Kahala and MTY units in the United States.