Investigating the effect of probiotics in the small intestine is particularly complex, due to its inaccessible location in the gastrointestinal tract. To overcome this challenge, we employed the high throughput ex vivo SIFR® technology, which is validated to provide predictive insights for clinical findings. We investigated the effects of a 9-species probiotic formula (Ecologic® 825) on the ileostoma microbiota of healthy humans. To account for interpersonal variation, we included six donors in the study. Microbial composition and metabolite production were analysed at 5 different time points, which facilitated the identification of correlations between dynamic changes in the microbial composition and metabolic fingerprints of the community. Notably, supplementation with the probiotic formula led to a decrease in ethanol production, associated with a reduction of pathobionts such as Enterococcaceae and Klebsiella pneumoniae. Additionally, the abundance of beneficial species such as Lactobacillaceae, Veillonella dispar and Anaestipes caccae resulted in a sharp increase in the levels of propionate, butyrate, and other health-related metabolites. The findings of this SIFR® study can be used to develop more effective treatments for a range of small intestinal conditions.