Probiotic encapsulation is an entire system that not only involves but also depends on many factors. Elements such as the encapsulation method itself, materials, environmental conditions, and last, but not least, the strain; all play an important role in the encapsulation process. The current paper focuses on the right selection of probiotics, the various stress factors that impact the survival capacity of probiotics during and after encapsulation, and the rational selection of appropriate protection strategies to overcome these factors and achieve the highest possible encapsulation efficiency under optimal conditions. This review discusses the effects of temperature, moisture content, and water activity as well as pH, oxygen, and pressure on the viabilities of microorganisms. The effect of the surface and structure of the capsules on the encapsulated microorganisms and the impact of the materials used for the encapsulation are discussed as well. Last, but not least, the importance of choosing the right bacteria is reviewed.