Candida albicans is a common commensal of the intestinal tract and vaginal mucosa, and the bacterial microbiota is essential to keep the fungus in this state. Lactobacillus species are potent members of the microbiota that contribute to this process. Antibiotics that eradicate lactobacilli, or diets that do not support their growth, predispose to C. albicans overgrowth and infection in experimental models and patients. These bacteria employ a myriad of mechanisms to antagonize C. albicans pathogenicity. Using in vitro and organ-on-chip models, combined with transcriptional profiling and metabolome analysis, we uncovered molecular mechanisms behind the antagonistic interactions of, in particular, Lactobacillus rhamnosus. We observed that, among other Lactobacillus species, L. rhamnosus antagonizes C. albicans pathogenicity on intestinal and vaginal epithelium. Although underlying mechanisms differ between both niches, a common denominator is a need for lactobacilli to proliferate to exert their protective effect. Both vaginal and intestinal epithelial cells were found to foster the growth of L. rhamnosus. On intestinal epithelium, TCA-cycle metabolites and gamma-glutamyl amino acids were identified as possible mediators supporting L. rhamnosus growth. When infecting L. rhamnosus-colonized intestinal epithelium, C. albicans mounts a metabolic stress response. Moreover, this response coincides with down-regulation of virulence genes and genes essential for fungal growth. L. rhamnosus proliferating on the epithelium produces metabolites known to be toxic for C. albicans as well as metabolites potentially capable of antagonizing pathogenicity. Collectively, we show that L. rhamnosus antagonizes C. albicans pathogenicity on different levels. Epithelial cells sustain L. rhamnosus colonization, which modulates the metabolic environment, but also influences the fungal transcriptional responses thereby suppressing pathogenicity mechanisms on a molecular level.