Long-chain polyunsaturated fatty acids, n-3 series (n-3 LC-PUFA), are known for their preventive effects against cardiovascular disease. In an unfavourable economic and environmental context of fish oil production, marine microalgae could be an alternative source of n-3 LC-PUFA and are of interest for human nutrition. The aim of this study was to evaluate the effects of P. tricornutum, a microalga rich in eicosapentaenoic acid and used as a food supplement, on the metabolic disorders associated with metabolic syndrome and obesity development. Three male Wistar rat groups (n = 6) were submitted for eight weeks to a standard diet or high-fat diet (HF) with 10% fructose in drinking water, supplemented or not with 12% of P. tricornutum (HF-Phaeo). Supplementation led to n-3 LC-PUFA enrichment of lipids in the liver, plasma and erythrocytes. Plasma transaminases showed no difference between the HF and HF-Phaeo groups. Body weight, fat mass, inflammatory markers and insulinemia decreased in HF-Phaeo rats versus the HF group. Plasma total cholesterol, triacylglycerols and leptine diminished in HF-Phaeo rats, while HDL-cholesterol increased. In conclusion, this study highlights the beneficial effects of P. tricornutum in reducing the metabolic disorders associated with metabolic syndrome.