Methods of increasing the amount of one or more functional compounds in medicinal mushroom biomass and mushroom mycelia by growing the mushrooms on a substrate that is high in the functional compound or compounds of interest is provided. More specifically, a method of increasing the amount of anthocyanins in mushrooms is provided. Mushrooms are grown on a substrate rich in anthocyanins, such as purple corn or other suitable red, purple or black-pigmented substrate, and incorporate the anthocyanins during growth. Mushrooms grown by this method, as well as methods of improving the growth rate and potency of mushrooms, are also provided.