This study investigated the effects of intestinal microbiota on the metabolism of geniposide by using a rat model treated with a mixture of antibiotics. The plasma concentration of geniposide was determined after oral administration in control and antibiotics-treated rats by using liquid chromatography–tandem mass spectrometry. The maximum plasma concentrations (Cmax) of geniposide in control and antibiotics-treated rats were 0.91 ± 0.26 and 1.01 ± 0.04 μg/mL, respectively, and the area under the curve (AUC) values were 7.34 ± 3.32 and 11.9 ± 2.1 μg·h/mL (p < 0.05), respectively. The levels of geniposide in rat feces were 0.64 and 15.6 mg, respectively, in the control and antibiotics-treated groups. Thus, the systemic exposure of geniposide was greater in the antibiotics-treated rats. This may be due to the antibiotic-induced suppression of the metabolic activities of the intestinal microbiota. These results suggest that the gut microbiota may have an impact on the bioavailability of geniposide.