The effect of inulin on isoflavone absorption and the effect of isoflavones and synergy with inulin on calcium absorption in rats was investigated. Rats (n = 48) were divided into three groups and fed inulin (50 mg/g), isoflavone (8 mg/g) or inulin + isoflavone (50 mg/g + 8 mg/g) diets for 21 days. After a 2-h fast, rats were given 45Ca orally or intraperitoneally, together with 25 mg of calcium as calcium acetate. Blood and femurs were collected 4 days later. Sera were analyzed for isoflavones using HPLC-MS, femurs for 45Ca by β-scintillation counting, and total femoral calcium by atomic absorption spectroscopy. Both groups fed isoflavones had similar and significantly higher weight-adjusted total femoral calcium content compared to the inulin-fed group (p < 0.0001). 45Ca absorption was significantly higher (p < 0.01) when isoflavones were added to the diet, and serum equol was significantly lower (p < 0.01) when inulin was added to the diet containing isoflavones. We conclude that isoflavones enhance calcium absorption, without synergy from inulin, and that inulin decreases equol production.