Small Intestinal Bacterial Overgrowth (SIBO) is a poorly understood disease characterized by the overgrowth of bacteria in the small intestine. The current treatment for SIBO is rifamycin antibiotics, a costly treatment with an average success rate of 60% and a relapse rate of 45%. This research focused on using Berberis vulgaris and Azadirachta indica, two plants known for their antimicrobial properties, as potential cost-effective alternatives. Extracts were derived from the plants using ethanol, water, and 1:1 ethanol-water dilutions. The extracts were tested using resazurin viability assays on representative bacteria associated with SIBO, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis, and Micrococcus luteus. Inhibition was compared to rifampicin, a rifamycin antibiotic. Extracts from both plant species demonstrated high efficacy amongst the extracts in effectively inhibiting bacterial growth in comparison to rifampicin. In addition, the extracts were not toxic to the yeast model Saccharomyces cerevisiae. Results of these assays suggest that the extracts are unlikely to be toxic to mammalian cells. The findings of this research also suggest that the extracts could offer a cost-effective, easily accessible, and efficient alternative to rifaximin in SIBO treatment, potentially improving patient quality of life.