The subject invention provides methods of producing advantageous microbes and/or by-products using a modified form of solid-state fermentation, or matrix fermentation. In particular, the methods utilize foodstuff mixed with liquid nutrient medium to produce a three-dimensional scaffold substrate having ample surface area on which the microbes can grow. The methods can be used to cultivate yeasts, fungi and bacteria at high concentrations without susceptibility to total contamination. The subject invention can be used in remote locations and can be transported with ease.