This study aimed to assess the probiotic potential of Enterococcus durans F21 and its microencapsulation. Two microencapsulation methods, spray-drying (SD) and freeze-drying (FD), were employed using sodium caseinate (Cas) as a cell protectant at concentrations of 0.035% and 1% and at two pHs, 3 and 7. Maltodextrins (MD) served as wall material (10%). Microcapsules were analysed for cell viability and membrane damage after drying, survival under simulated gastro-intestinal conditions, antimicrobial activity, stability during storage, and physicochemical characterization. Results showed that E. durans F21 exhibited promising probiotic properties, including moderate auto-aggregation, high co-aggregation with pathogens, moderate biofilm formation, and resistance to simulated gastrointestinal conditions. The encapsulation pH showed to be a crucial factor affecting the viability of microencapsulated cells. Microencapsulation at pH 3 adversely affected cell viability during drying. However, microencapsulation at pH 7 using Cas (at 0.035 and 1%) was found to be most effective in maintaining higher cell viability under similar conditions. No significant difference was detected between both Cas formulations, suggesting that 0.035% Cas concentration might be sufficient for the microencapsulation process at pH 7. Moreover, FD proved to be the most effective method to produce E. durans F21 microcapsules with high viability (cell viability of 93%) and stability during storage (cell viability of 99%). Conclusively, microencapsulation of E. durans F21 using Cas, at pH 7, and employing FD method could be a promising strategy for producing highly viable microcapsules containing E. durans F21 cells with high probiotic and bio-preservative potentials in foods.