The present invention provides a method for the preparation of a myceliated cacao bean or other agricultural product. This method includes providing cacao beans or other agricultural substrate, optionally hydrating the cacao beans or other agricultural product, and optionally pasteurizing or sterilizing the cacao beans or other agricultural substrate to provide prepared cacao beans or other agricultural substrate, and a step of inoculating the prepared cacao beans or other agricultural substrate with a prepared fungal component and culturing the inoculated cacao beans or other agricultural substrate to prepare the myceliated product. The methods of the instant invention result in prepared cacao beans or other agricultural substrate having reduced levels of undesirable taste components, such as theobromine, catechin, epicatechin, gallic acid equivalents, and/or 2-methoxy-3-isopropylpyrazine, and increased levels of myceliation products, such as fungal β-glucans, chitin, proteins, glycoproteins, pyrazines and polysaccharides, relative to starting cacao beans or other agricultural substrate.