Inspired by the rampant digestive disorders and the vast bacterial infections, this study aimed at fabricating nanofibers made of inulin/polyvinyl alcohol (PVA) composite nanofibers (CNFs) using the electrospinning technique and testing their prebiotic and antibacterial activities. The inulin/PVA CNFs were tested for prebiotic activity with Lactobacillus species while Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) were used to assess the antibacterial potentiality. During the fabrication of the CNFs, different electrospinning parameters have been carefully controlled, in order to produce nanofibers with relatively uniform diameter, fewer beads, and high integrity. The different parameters included variable solution concentration (material ratio varied from 14 to 20 wt %), applied voltage (varied from 15 to 25 kV), and solution flow (ranged between 0.005 and 0.5 mL/min). The chemical characteristics, thermal stability, and morphology of the formed CNFs were comprehensively characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, and scanning electron microscopy. Selected CNFs, showing the best diameter uniformity and integrity, were tested for the prebiotic and antimicrobial activity. A 38% increase in prebiotic activity of CNFs, compared to their bulk solution, was observed. The antibacterial activity of the selected CNFs was enhanced, from ∼40% (pure inulin) to 70% (inulin/PVA CNFs) against E. coli and 45% against S. aureus. This study investigates the prebiotic and antibacterial activities of PVA/inulin CNFs and provides the foundation for inulin/PVA CNF use in the healthcare sector, as in disinfectants and/or digestive disorders.