Medical applications of nanotechnology are promising in creating efficient and targeted therapies. However, so far, nanodrug design has not taken into consideration possible effects on human microbiota. The beneficial functions of bacteria could be stimulated by nanodrugs while negative effects on beneficial bacteria could cause risks to human health. Here, simulated intestinal fluid (IF) was optimized for culturing a human commensal and probiotic bacterial strain, Lactobacillus casei, to study the effects of medically relevant NPs—Ag and hyaluronic acid-coated Au NPs (HA-Au NPs)—in conditions pertinent to the gastrointestinal tract. When cultivated either aerobically or anaerobically, the specific growth rates of L. casei were ~0.2 h−1 in IF and ~0.4 h−1 in the standard medium of lactobacilli (MRS). Ag NPs inhibited the growth of L. casei in IF at lower concentrations (EC50 ~ 65 and 15 mg/L in aerobic and anaerobic conditions, respectively) than in MRS (EC50 > 100 mg/L), likely caused by differences in the composition of the two media and different intrinsic growth rates of bacteria in IF and MRS. Ag NP dissolution in IF and MRS did not explain the differences in growth inhibition, implying NP-specific effects. HA-Au NPs were not growth-inhibitory to L. casei up to 250 mg/L. Still, both NPs at sub-growth-inhibitory concentrations suppressed the expression of bacteriocin genes in L. casei, suggesting an inhibitory effect of NPs on the probiotic properties of L. casei, i.e., its competitiveness in microbial communities. However, HA-Au NPs did not appear to affect or even stimulated the immunomodulatory properties of L. casei in human intestinal epithelial cells. Thus, medically relevant NPs at low, sub-bacteriostatic levels can affect the metabolism of beneficial human bacteria and potentially induce changes in the microbiota and immune signaling.