The production of biomolecules using agro-industrial by-products as feedstock is a growing trend worldwide. Selenium (Se) is a trace element essential for health, and the Se-enrichment of yeast biomass can enhance its benefits. This study investigated the feasibility of the production of Saccharomyces cerevisiae Se-enriched biomass using a medium composed of corn bran and soybean bran acid hydrolysates as carbon and nitrogen sources in a stirred-tank reactor. After hydrolysis, hydrolysates presented complex composition and high concentrations of sugars, proteins, and minerals. The use of a stirred-tank bioreactor leads to the production of 9 g/L S. cerevisiae biomass enriched with 236.93 μg/g Se, and 99% cell viability. Likewise, the combination of sugarcane molasses and soybean bran hydrolysate was effective for cell growth of a probiotic strain of S. cerevisiae with a 24.08% β-glucan content. The results demonstrated that starchy acid hydrolysates are low-cost and efficient substrates for the production of yeast biomass and derivate products and may contribute to further studies for a sustainable development of biorefinery technologies.