Plant fertilization is a major issue in the context of increasing population and food risk, higher cost of fertilizers, and low target efficiency of traditional mineral fertilization practices. Alternatively, application of microbial inoculants to the soil can enhance the uptake of nutrients by plants and increase the efficiency of mineral fertilizers and manures. Encapsulation methods involve covering and protecting the microorganisms. Encapsulation of bacterial cells has been challenged and used mainly in the agricultural industry using processes, such as spray drying, interfacial polymerization, or cross-linking. Here, we review techniques for microbial inoculants and their benefits for sustainable agriculture. Techniques include fluidized bed, extrusion, molecular inclusion, coacervation, liposomes, ionic or inverse gelation, and oil-entrapped emulsion. Major topics discussed are formulation of microbial inoculants, conventional inoculants, bioencapsulation materials, bioencapsulation techniques, and future trends. We found that (1) conventional inoculant does not provide adequate protection for microorganisms. (2) Bioencapsulation improves the protection and controlled release of bacteria. (3) Sodium alginate is one of the most used products for the bioencapsulation of microorganisms. (4) The bioencapsulation of microbial inoculants is performed with the incorporation of an active ingredient into a matrix followed by a mechanical operation, and finally stabilization by a chemical or physical-chemical process. (5) Spray-drying process works on a continuous basis, low operating cost, and high quality of capsules in good yield, although the high temperature used in the process is not very appropriate for encapsulating non-spore-forming bacteria. 6) Fluid-bed process is a promising encapsulation technique for large-scale production in agricultural industry. (7) Ionic gelation is currently the most adequate method found to encapsulate bacteria. (8) Some advantages and drawbacks are found for each technique; therefore, the selection of suitable bioencapsulation method will depend on bacteria strain, cost, processing conditions, and handling.