Microencapsulation, as one of the synergistic methods, has shown significant effects on probiotic survival. The main objective of the present study was to examine the effect of bael pulp waste pectin as a prebiotic on the survivability of two probiotics (Bacillus clausii and Saccharomyces boulardii) individually under simulated digestive conditions after microencapsulation. Probiotics were microencapsulated with and without pectin (used as a control) by the extrusion method. Furthermore, the encapsulation efficiency of the beads was examined and the viability of probiotics along with moisture content and swelling behavior, was evaluated by subjecting beads to different artificial gastrointestinal conditions and compared with the control beads. As a result, encapsulation with prebiotic pectin exhibited a significant (P < 0.05) effect on the survivability of B. clausii and S. boulardii. Probiotics microencapsulated with pectin seemed to be more stable at refrigeration temperature compared to probiotics microencapsulated without pectin for up to 30 days of storage. Therefore, it was concluded that the bael pulp waste pectin could be used as an effective prebiotic for the development of synbiotic products.