Invasive bacterial gastrointestinal infections represent a substantial clinical burden worldwide, contributing to significant morbidity and, in severe cases, mortality. The causative bacterial agents of these infections include Shigella spp., enteroinvasive Escherichia coli, Salmonella spp., Campylobacter jejuni, Yersinia enterocolitica, and Listeria monocytogenes. Given the growing challenges of therapy failures and rising antibiotic resistance, there is still an unmet need to identify novel, effective, and safe compounds exhibiting antimicrobial, anti-inflammatory, and immunomodulatory activities. In the present review, we aimed to compile current data regarding three alkaloids-berberine, sanguinarine, and cheleritrin-which hold significant promise in treating bacterial invasive gastrointestinal diseases. Our review extended beyond the direct antimicrobial properties of these compounds against pathogens capable of breaching the intestinal epithelial barrier. We also presented their modulatory effects on intestinal barrier integrity and their influence on the composition and function of the resident gut microbiota, thereby highlighting their potential indirect role in attenuating pathogen invasion and disease progression. Thus, our review presents alkaloids as potential preparations that potentiate the activity of classic anti-infective drugs, as well as substances that, by affecting the microbiome and intestinal mucosa, could be used for inflammatory bowel diseases.