Probiotics, particularly yeasts from the genus Saccharomyces, are valuable for their health benefits and potential as antibiotic alternatives. To be effective, these microorganisms must withstand harsh environmental conditions, necessitating advanced protective technologies such as encapsulation to maintain probiotic viability during processing, storage, and passage through the digestive system. This review and meta-analysis aims to describe and compare methods and agents used for encapsulating Saccharomyces spp., examining operating conditions, yeast origins, and species. It provides an overview of the literature on the health benefits of nutritional yeast consumption. A bibliographic survey was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. The meta-analysis compared encapsulation methods regarding their viability after encapsulation and exposure to the gastrointestinal tract. Nineteen studies were selected after applying inclusion/exclusion criteria. Freeze drying was found to be the most efficient for cell survival, while ionic gelation was best for maintaining viability after exposure to the gastrointestinal tract. Consequently, the combination of freeze drying and ionic gelation proved most effective in maintaining high cell viability during encapsulation, storage, and consumption. Research on probiotics for human food and animal feed indicates that combining freeze drying and ionic gelation effectively protects Saccharomyces spp.; however, industrial scalability must be considered. Reports on yeast encapsulation using agro-industrial residues as encapsulants offer promising strategies for preserving potential probiotic yeasts, contributing to the environmental sustainability of industrial processes.