The reputation of Flying Dog beers grew quickly, and demand soon exceeded the brewpub’s capacity. So, in 1994 Flying Dog opened a 50-barrel brewery in Denver, Colorado from which its ales were distributed to 31 states of the United States.
In May 2006, Flying Dog acquired the Wild Goose brand when they purchased the Frederick Brewing Company located in Frederick, Maryland, and in January 2008 all production was moved to the Maryland facility. According to their web site, this location is where "70% of Flying Dog Beer is already being brewed." Accounting, sales, marketing and other administrative functions have remained largely unaffected by this change and their headquarters remains in Denver. Currently, the brewery has a capacity to brew 100,000 barrels of beer per year.
In December 2010, the Logan Shaw Brewing Company purchased the Wild Goose brand from Flying Dog Brewery, with plans to pair Wild Goose beers with their own craft brews.
Flying Dog Brewery is noted for using the unusual art of Ralph Steadman, best known as the illustrator of the works of Hunter S. Thompson, on its labels. In 2005, the brewery created a new beer in Thompson’s  honor, Gonzo Imperial Porter . Initially in limited-release in 750mL bottles, the Gonzo Imperial Porter is now one of the regular offerings of the brewery.