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The development of functional food products is increasingly gaining lots of interest and popularity among stakeholders. The aim of this study was to evaluate the bioaccessibility of three <i>Lactobacillus</i> sp. starter cultures, including <i>Lacticaseibacillus casei</i> KKU-KK1, <i>Lactiplantibacillus pentosus</i> KKU-KK2, and <i>Lactobacillus acidophilus</i> KKU-KK3, in order to enhance the performance of the probiotic potential of <i>Nham</i> protein hydrolysates in Thai fermented sausage using microencapsulation technology. Probiotic microcapsules were created from a novel wall material made up of a combination of glutinous rice flour and inulin through a freeze-drying process. Accordingly, the results of three formulations of <i>Nham</i> probiotic and spontaneous fermentation (control) characterized by their physicochemical and microbiological characteristics displayed a correlation between an increase in the amount of total acidity, the population of lactic acid bacteria, and the generated TCA-soluble peptides, while the pH and total soluble protein gradually decreased under proteolysis during the fermentation time. The fractionation of <i>Nham</i> protein hydrolysates (NPHs) was prepared using a microwave extraction process: NPH-<i>nham</i>1, NPH-<i>nham</i>2, and NPH-<i>nham</i>3 (10 mg/mL with fermentation time 114 h), exhibited the highest DPPH radical-scavenging activity and FRAP-reducing power capacity as well, compared to NPH-<i>nham</i>_control at <i>p</i> < 0.05. Moreover, those NPHs peptides showed dose-dependent inhibiting of selected pathogenic bacteria (<i>E. coli</i> TISTR 073, <i>S. aureus</i> TISTR 029, and <i>Ent. aerogenes</i> TISTR 1540). Anti-microbial properties of NPHs peptides against gram-negative bacteria were higher than against gram-positive bacteria. In conclusion, the bioaccessibility of NPHs peptides was significantly enhanced by micro-encapsulation and showed a potential bioactive characteristic for developing into a probiotic agent.