Conventional microalgal drying consumes huge time and contributes to 60–80% of downstream process costs. With the aim to develop an effective and rapid drying process, the present study evaluated the performance of microwave based drying (MWD) with a power range of 360–900 W and compared with the conventional oven drying (OD) at 40–100 °C. MWD was found to be efficient due to uniform and volumetric heating because of dipolar interaction, with an effective diffusivity of 0.47 × 10−9−1.63 × 10−9 m2 s−1, comparatively higher than OD. Activation and specific energy of 32.43 W g−1 and 42.9–56.07 kWh kg−1 was projected respectively, and a falling rate period with best fit for Newton and Henderson-Pabis model was observed for MWD. Uniform heating from internal sub-surface avoided cell distress, resulting in 14.4% higher lipid yield and significant preservation of biochemical components that can be processed into bioenergy and valuable products in microalgal biorefinery.