This paper examines the impact of inulin, Lactobacillus spp. (candidate probiotics), and synbiotic (inulin + Lactobacillus spp.) preparation on oxalate degrading activity and viability of Escherichia coli. In this study, the lowest viability of E. coli was recorded for the synbiotic treatments of Lactobacillus fermentum BP5 (59%) and IP5 (60%). The oxalate degrading activity of L. fermentum IP5 was 38.18 and 29.60% higher than the other strains after growth in 10 mM and 20 mM MRS-ox plus 5% inulin media, respectively. The mixture of three strains demonstrated higher oxalate degrading capacity than the individual strains and showed the same good growth rates (9.43 CFU mL−1) as individuals. The study concludes that the addition of prebiotics has a significant effect on probiotics; therefore, a combination of L. fermentum IP5 with inulin could be a viable probiotic-based functional food approach in administering oxalate metabolism and also treatment of E. coli-related infections.