Stone Brewing was founded by Greg Koch and Steve Wagner in 1996 in San Marcos, California. Local designer/illustrator Thomas K. Matthews created their (now famous gargoyle) logo. He also drew the Arrogant Bastard Ale, Stone Ruination IPA and Stone Levitation Ale gargoyles, as well as barley and hops motifs.
In 2006, Stone relocated from the original brewery to a new, custom-designed facility in Escondido, California. In 2008, Stone Brewing covered the roof with solar panels and cut their energy costs nearly in half. In 2013, the company opened a new packaging hall just south of the brewery to house their bottling and keg lines. The brewery also has a Stone Company Store which sells merchandise as well as Stone's year-round beers and special releases.
In 2016, Stone opened a brewery and Stone Company Store in Richmond, Virginia -- its first location in the eastern United States. In June 2022, Sapporo Bewing (Japan) purchased Stone Brewing.