Forty-eight male Wistar rats were fed diets containing low (0.051% of diet) or high (0.153% of diet) levels of an ellagitannin-rich (ET) strawberry extract with dietary fructooligosaccharides (FOS) or cellulose (CEL) for 4 weeks. The in vivo study demonstrated that some positive changes in the cecal metabolism resulting from the ingestion of a diet enriched only with FOS were completely or slightly suppressed by the dietary ET. In particular, the pH value (7.21 vs 7.36), short-chain fatty acid production (41.2 vs 30.0 μmol/100g BW), and β-glucuronidase activity (20.2 vs 15.7 μmol/h/g) in the cecum of rats fed with FOS were affected upon the addition of the ET extract. Dietary FOS caused higher metabolism of the tested ET strawberry extract in the gastrointestinal tract of rats. Moreover, the systemic effect of the supplements when consumed together showed undesired serum HDL-cholesterol decrease (0.78 vs 1.02 mmol/L in the treatment with FOS only).