Marine-based food supplements can improve human nutrition. In an effort to modulate glycaemic response and enhance nutritional aspects, marine-derived algal food rich in astaxanthin was used in the formulation of a model food (wholemeal cookie). Astaxanthin substitution of cookies made from three flours (wheat, barley and oat) demonstrated a significant reduction in the rate of glucose released during in vitro digestion together with an increase in the total phenolic content (TPC) and antioxidant capacity of the food. The significantly (p < 0.005) lower free glucose release was observed from cookies with 15% astaxanthin, followed by 10% and then 5% astaxanthin in comparison with control cookies of each flour. Total phenolic content, DPPH radical scavenging and Oxygen Radical Absorbance Capacity (ORAC) value also notably increased with increase in astaxanthin content. The results evidence the potential use of microalgae to enhance the bioactive compounds and lower the glycaemic response of wholemeal flour cookie.