In the current study, apple-pectin-based novel nanofibers were fabricated by electrospinning. Polyvinyl alcohol (PVA) and apple pectin (PEC) solution were mixed to obtain an optimized ratio for the preparation of electrospun nanofibers. The obtained nanofibers were characterized for their physiochemical, mechanical and thermal properties. The nanofibers were characterized using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and thermogravimetric analysis (TGA). Furthermore, an assay of the in vitro viability of free and encapsulated probiotics was carried out under simulated gastrointestinal conditions. The results of TGA revealed that the PVA/PEC nanofibers had good thermal stability. The probiotics encapsulated by electrospinning showed a high survival rate as compared to free cells under simulated gastrointestinal conditions. Furthermore, encapsulated probiotics and free cells showed a 3 log (cfu/mL) and 10 log (cfu/mL) reduction, respectively, from 30 to 120 min of simulated digestion. These findings indicate that the PVA/PEC-based nanofibers have good barrier properties and could potentially be used for the improved viability of probiotics under simulated gastrointestinal conditions and in the development of functional foods.