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 Lactobacillus sp. starter cultures, including Lacticaseibacillus casei KKU-KK1, Lactiplantibacillus pentosus KKU-KK2, and Lactobacillus acidophilus KKU-KK3, in order to enhance the performance of the probiotic potential of Nham 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 Nham 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 Nham protein hydrolysates (NPHs) was prepared using a microwave extraction process: NPH-nham1, NPH-nham2, and NPH-nham3 (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-nhamcontrol at p < 0.05. Moreover, those NPHs peptides showed dose-dependent inhibiting of selected pathogenic bacteria (E. coli TISTR 073, S. aureus TISTR 029, and Ent. aerogenes 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.