On the microbiota of healthy people, the impact of putatively probiotic Fermented Milk (FM) with buriti pulp (FMB), passion fruit pulp (FMPF), or without fruit pulp (FMC) was assessed. FM formulations were injected into a SHIME simulator of the human intestinal microbial environment to measure the presence of Short Chain Fatty Acids (SCFA), Lactic Acid Bacteria (LAB), microbiota makeup, and ammonium ions. The inclusion of the fruit pulp had an impact on the probiotic LAB viability in FM. Bifidobacterium was connected to FM formulations, while Alistipes was connected to FMPF and FMB, and Lactobacillus and Lacticaseibacillus were predominate in FMC samples. Phocaeicola was dominating in the FMPF and FMB samples. While Mediterraneibacter served as the primary component of the FMPF and FMB networks, trabulsiella served as the primary component of the FMC. Acetic acid levels were raised by the FM formulations, and the FMB treatment revealed notably high levels of propionic and butyric acids. Compared to the control, all FM formulations reduced the ammonium ions, but the FMPF samples stood out since they contained less ammonia. The fruit pulp infused probiotic FM.