Probiotic supplementation can mitigate hepatic injury, but the low survival rate of probiotics through the gastrointestinal tract limits their therapeutic efficacy. This study aimed to enhance the viability of Pediococcus acidilactici (P. acidilactici) by encapsulating it in an alginate-pectin matrix coated with chitosan (APC) and to evaluate the hepatoprotective effects of the encapsulated probiotic in a rat model of bile duct ligation (BDL)-induced hepatic fibrosis. APC microcapsules were fabricated using an extrusion technique and characterized by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) to confirm successful encapsulation. The survival of encapsulated and non-encapsulated P. acidilactici was assessed in simulated gastrointestinal fluids. For in vivo evaluation, forty-eight rats were randomly assigned to six groups and treated for 28 days. Outcomes included serum bilirubin and liver enzyme levels, hepatic oxidative stress markers, histopathological changes, and expression of fibrosis- and inflammation-related genes measured by quantitative reverse transcription PCR (RT-qPCR). Encapsulation significantly improved probiotic viability in gastrointestinal conditions (5.15 ± 0.21 vs. 2.05 ± 0.35 log₁₀ CFU/mL after two hours, P ≤ 0.05). In BDL rats, treatment with encapsulated P. acidilactici led to significant reductions in serum bilirubin, liver enzymes, and oxidative stress, alongside improved liver histology and favorable modulation of gene expression compared to controls (P ≤ 0.05). These findings demonstrate that APC encapsulation enhances the gastrointestinal stability of P. acidilactici and supports its therapeutic potential against hepatic fibrosis.